VCV000492006.3 - ClinVar

NM_001048174.2(MUTYH):c.1176_1177delinsTT (p.Leu392_Leu393=)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(1)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Likely benign

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001048174.2(MUTYH):c.1176_1177delinsTT (p.Leu392_Leu393=)

Variation ID: 492006 Accession: VCV000492006.3

Type and length

Indel, 2 bp

Location

Cytogenetic: 1p34.1 1: 45331482-45331483 (GRCh38) [ NCBI UCSC ] 1: 45797154-45797155 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Feb 19, 2018	Dec 11, 2022	Jul 19, 2017

HGVS

Nucleotide	Protein	Molecular consequence
NM_001048174.2:c.1176_1177delinsTT MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001041639.1:p.Leu392_Leu393=	synonymous
NM_001128425.2:c.1260_1261delinsTT MANE Plus Clinical Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001121897.1:p.Leu420_Leu421=	synonymous
NM_001048171.2:c.1176_1177delinsTT	NP_001041636.2:p.Leu392_Leu393=	synonymous
NM_001048172.2:c.1179_1180delinsTT	NP_001041637.1:p.Leu393_Leu394=	synonymous
NM_001048173.2:c.1176_1177delinsTT	NP_001041638.1:p.Leu392_Leu393=	synonymous
NM_001293190.2:c.1221_1222delinsTT	NP_001280119.1:p.Leu407_Leu408=	synonymous
NM_001293191.2:c.1209_1210delinsTT	NP_001280120.1:p.Leu403_Leu404=	synonymous
NM_001293192.2:c.900_901delinsTT	NP_001280121.1:p.Leu300_Leu301=	synonymous
NM_001293195.2:c.1176_1177delinsTT	NP_001280124.1:p.Leu392_Leu393=	synonymous
NM_001293196.2:c.900_901delinsTT	NP_001280125.1:p.Leu300_Leu301=	synonymous
NM_001350650.2:c.831_832delinsTT	NP_001337579.1:p.Leu277_Leu278=	synonymous
NM_001350651.2:c.831_832delinsTT	NP_001337580.1:p.Leu277_Leu278=	synonymous
NM_001407069.1:c.1209_1210delinsTT	NP_001393998.1:p.Leu403_Leu404=	synonymous
NM_001407070.1:c.1176_1177delinsTT	NP_001393999.1:p.Leu392_Leu393=	synonymous
NM_001407071.1:c.1179_1180delinsTT	NP_001394000.1:p.Leu393_Leu394=	synonymous
NM_001407072.1:c.1176_1177delinsTT	NP_001394001.1:p.Leu392_Leu393=	synonymous
NM_001407073.1:c.1176_1177delinsTT	NP_001394002.1:p.Leu392_Leu393=	synonymous
NM_001407075.1:c.1092_1093delinsTT	NP_001394004.1:p.Leu364_Leu365=	synonymous
NM_001407077.1:c.1209_1210delinsTT	NP_001394006.1:p.Leu403_Leu404=	synonymous
NM_001407078.1:c.1179_1180delinsTT	NP_001394007.1:p.Leu393_Leu394=	synonymous
NM_001407079.1:c.1137_1138delinsTT	NP_001394008.1:p.Leu379_Leu380=	synonymous
NM_001407080.1:c.1134_1135delinsTT	NP_001394009.1:p.Leu378_Leu379=	synonymous
NM_001407081.1:c.1176_1177delinsTT	NP_001394010.1:p.Leu392_Leu393=	synonymous
NM_001407082.1:c.831_832delinsTT	NP_001394011.1:p.Leu277_Leu278=	synonymous
NM_001407083.1:c.1218_1219delinsTT	NP_001394012.1:p.Leu406_Leu407=	synonymous
NM_001407085.1:c.1218_1219delinsTT	NP_001394014.1:p.Leu406_Leu407=	synonymous
NM_001407086.1:c.1179_1180delinsTT	NP_001394015.1:p.Leu393_Leu394=	synonymous
NM_001407087.1:c.1197_1198delinsTT	NP_001394016.1:p.Leu399_Leu400=	synonymous
NM_001407088.1:c.1176_1177delinsTT	NP_001394017.1:p.Leu392_Leu393=	synonymous
NM_001407089.1:c.1176_1177delinsTT	NP_001394018.1:p.Leu392_Leu393=	synonymous
NM_001407091.1:c.900_901delinsTT	NP_001394020.1:p.Leu300_Leu301=	synonymous
NM_012222.3:c.1251_1252delinsTT	NP_036354.1:p.Leu417_Leu418=	synonymous
NR_146882.2:n.1404_1405delinsTT		non-coding transcript variant
NR_146883.2:n.1253_1254delinsTT		non-coding transcript variant
NR_176269.1:n.1400_1401delinsTT		non-coding transcript variant
NR_176270.1:n.1340_1341delGCinsTT
NR_176271.1:n.1263_1264delinsTT		non-coding transcript variant
NR_176272.1:n.1327_1328delinsTT		non-coding transcript variant
NR_176273.1:n.1285_1286delinsTT		non-coding transcript variant
NR_176274.1:n.1340_1341delinsTT		non-coding transcript variant
NC_000001.11:g.45331482_45331483delinsAA
NC_000001.10:g.45797154_45797155delinsAA
NG_008189.1:g.13988_13989delinsTT
LRG_220:g.13988_13989delinsTT
LRG_220t1:c.1260_1261delGCinsTT	LRG_220p1:p.Leu420_Leu421=

... more HGVS ... less HGVS

Protein change

Other names

Canonical SPDI

NC_000001.11:45331481:GC:AA

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA658683142 dbSNP: rs1553125790 VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
MUTYH		-	-	GRCh38 GRCh37	2688	2844

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Hereditary cancer-predisposing syndrome	Likely benign (1)	criteria provided, single submitter	Jul 19, 2017	RCV000581151.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Likely benign (Jul 19, 2017)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Hereditary cancer-predisposing syndrome Affected status: unknown Allele origin: germline	Color Diagnostics, LLC DBA Color Health Accession: SCV000690510.2 First in ClinVar: Feb 19, 2018 Last updated: Dec 11, 2022

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs1553125790 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Dec 25, 2023

ClinVar Genomic variation as it relates to human health

NM_001048174.2(MUTYH):c.1176_1177delinsTT (p.Leu392_Leu393=)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs1553125790 ...