NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter) AND not specified

Germline classification:: Benign (1 submission)
Last evaluated:: Oct 28, 2020
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001777158.9

Allele description [Variation Report for NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter)]

NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter)

Genes:

CCDST:cervical cancer associated DHX9 suppressive transcript [Gene - HGNC]
FLG:filaggrin [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q21.3

Genomic location:

Preferred name:

NM_002016.2(FLG):c.5717C>A (p.Ser1906Ter)

HGVS:

NC_000001.11:g.152309169G>T
NG_016190.1:g.21035C>A
NM_002016.2:c.5717C>AMANE SELECT
NP_002007.1:p.Ser1906Ter
NP_002007.1:p.Ser1906Ter
LRG_1028t1:c.5717C>A
LRG_1028:g.21035C>A
LRG_1028p1:p.Ser1906Ter
NC_000001.10:g.152281645G>T
NM_002016.1:c.5717C>A

Protein change:

S1906*

Links:

dbSNP: rs141784184

NCBI 1000 Genomes Browser:

rs141784184

Molecular consequence:

NM_002016.2:c.5717C>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002014631	H3Africa Consortium - H3Africa	criteria provided, single submitter (Choudhury A et al. (Nature 2020))	Benign (Oct 28, 2020)	germline	research	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002014631

H3Africa Consortium - H3Africa

criteria provided, single submitter

(Choudhury A et al. (Nature 2020))

Benign
(Oct 28, 2020)

germline

research

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	research

Citations

PubMed

High-depth African genomes inform human migration and health.

Choudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T, Wells G, Kumuthini J, Shriner D, Fakim YJ, Ghoorah AW, Dareng E, Odia T, Falola O, Adebiyi E, Hazelhurst S, Mazandu G, Nyangiri OA, Mbiyavanga M, Benkahla A, Kassim SK, Mulder N, et al.

Nature. 2020 Oct;586(7831):741-748. doi: 10.1038/s41586-020-2859-7. Epub 2020 Oct 28. Erratum in: Nature. 2021 Apr;592(7856):E26. doi: 10.1038/s41586-021-03286-9.

PubMed [citation]

PMID:: 33116287
PMCID:: PMC7759466

Details of each submission

From H3Africa Consortium - H3Africa, SCV002014631.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

Description

While the frequency of the alternate allele in gnoMAD v2.0.2 is 0.051, its frequency in African populations is >5%. This suggests that previous classifications of this variant as pathogenic are in error.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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Relating variation to medicine