NM_170707.4(LMNA):c.513+2T>G AND Cardiovascular phenotype

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jul 21, 2022
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:: RCV000618096.4

Allele description [Variation Report for NM_170707.4(LMNA):c.513+2T>G]

NM_170707.4(LMNA):c.513+2T>G

Genes:

LOC126805877:MED14-independent group 3 enhancer GRCh37_chr1:156099693-156100892 [Gene]
LMNA:lamin A/C [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1q22

Genomic location:

Preferred name:

NM_170707.4(LMNA):c.513+2T>G

HGVS:

NC_000001.11:g.156130775T>G
NG_008692.2:g.53203T>G
NG_082201.1:g.974T>G
NM_001257374.3:c.177+2T>G
NM_001282624.2:c.270+2T>G
NM_001282625.2:c.513+2T>G
NM_001282626.2:c.513+2T>G
NM_001406983.1:c.513+2T>G
NM_001406984.1:c.513+2T>G
NM_001406985.1:c.513+2T>G
NM_001406986.1:c.270+2T>G
NM_001406987.1:c.270+2T>G
NM_001406988.1:c.216+2T>G
NM_001406989.1:c.177+2T>G
NM_001406990.1:c.-45-3628T>G
NM_001406991.1:c.513+2T>G
NM_001406992.1:c.513+2T>G
NM_001406993.1:c.-46+2T>G
NM_001406994.1:c.-152+2T>G
NM_001406995.1:c.-45-3628T>G
NM_001406996.1:c.-46+2T>G
NM_001406997.1:c.-46+2T>G
NM_001406998.1:c.177+2T>G
NM_001406999.1:c.-152+2T>G
NM_001407000.1:c.-152+2T>G
NM_001407001.1:c.-151-3628T>G
NM_001407002.1:c.-45-3628T>G
NM_001407003.1:c.-46+2T>G
NM_005572.4:c.513+2T>G
NM_170707.4:c.513+2T>GMANE SELECT
NM_170708.4:c.513+2T>G
LRG_254t2:c.513+2T>G
LRG_254:g.53203T>G
NC_000001.10:g.156100566T>G
NM_170707.2:c.513+2T>G

Links:

dbSNP: rs1553264668

NCBI 1000 Genomes Browser:

rs1553264668

Molecular consequence:

NM_001406990.1:c.-45-3628T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001406995.1:c.-45-3628T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407001.1:c.-151-3628T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001407002.1:c.-45-3628T>G - intron variant - [Sequence Ontology: SO:0001627]
NM_001257374.3:c.177+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001282624.2:c.270+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001282625.2:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001282626.2:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406983.1:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406984.1:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406985.1:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406986.1:c.270+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406987.1:c.270+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406988.1:c.216+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406989.1:c.177+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406991.1:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406992.1:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406993.1:c.-46+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406994.1:c.-152+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406996.1:c.-46+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406997.1:c.-46+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406998.1:c.177+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001406999.1:c.-152+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407000.1:c.-152+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_001407003.1:c.-46+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_005572.4:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_170707.4:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]
NM_170708.4:c.513+2T>G - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000735383	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely pathogenic (Jul 21, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000735383

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely pathogenic
(Jul 21, 2022)

germline

clinical testing

Citation Link

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	clinical testing

Details of each submission

From Ambry Genetics, SCV000735383.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

The c.513+2T>G intronic variant results from a T to G substitution two nucleotides after coding exon 2 in the LMNA gene. This nucleotide position is highly conserved in available vertebrate species. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as likely pathogenic.

#	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: May 1, 2024

ClinVar

Relating variation to medicine