rs56199702
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_000165.5(GJA1):c.-16-12T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0063 in 1,546,168 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000165.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GJA1 | NM_000165.5 | c.-16-12T>A | intron_variant | Intron 1 of 1 | ENST00000282561.4 | NP_000156.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GJA1 | ENST00000282561.4 | c.-16-12T>A | intron_variant | Intron 1 of 1 | 1 | NM_000165.5 | ENSP00000282561.3 | |||
GJA1 | ENST00000647564.1 | c.-16-12T>A | intron_variant | Intron 1 of 1 | ENSP00000497565.1 | |||||
GJA1 | ENST00000649003.1 | c.-16-12T>A | intron_variant | Intron 1 of 1 | ENSP00000497283.1 | |||||
GJA1 | ENST00000650427.1 | c.-16-12T>A | intron_variant | Intron 1 of 1 | ENSP00000497367.1 |
Frequencies
GnomAD3 genomes AF: 0.00559 AC: 850AN: 152188Hom.: 8 Cov.: 32
GnomAD3 exomes AF: 0.00573 AC: 1433AN: 250014Hom.: 17 AF XY: 0.00571 AC XY: 773AN XY: 135340
GnomAD4 exome AF: 0.00638 AC: 8894AN: 1393862Hom.: 59 Cov.: 26 AF XY: 0.00638 AC XY: 4451AN XY: 697682
GnomAD4 genome AF: 0.00558 AC: 850AN: 152306Hom.: 8 Cov.: 32 AF XY: 0.00534 AC XY: 398AN XY: 74482
ClinVar
Submissions by phenotype
not provided Benign:3
GJA1: BS2 -
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Hypoplastic left heart syndrome 1 Uncertain:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -
Oculodentodigital dysplasia Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Syndactyly type 3 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at