rs1764389
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_002060.3(GJA4):c.132G>A(p.Val44=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.207 in 1,613,864 control chromosomes in the GnomAD database, including 38,345 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.26 ( 6388 hom., cov: 32)
Exomes 𝑓: 0.20 ( 31957 hom. )
Consequence
GJA4
NM_002060.3 synonymous
NM_002060.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0420
Genes affected
GJA4 (HGNC:4278): (gap junction protein alpha 4) This gene encodes a member of the connexin gene family. The encoded protein is a component of gap junctions, which are composed of arrays of intercellular channels that provide a route for the diffusion of low molecular weight materials from cell to cell. Mutations in this gene have been associated with atherosclerosis and a higher risk of myocardial infarction. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.63).
BP7
?
Synonymous conserved (PhyloP=-0.042 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.434 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJA4 | NM_002060.3 | c.132G>A | p.Val44= | synonymous_variant | 2/2 | ENST00000342280.5 | |
GJA4 | XM_005270750.3 | c.132G>A | p.Val44= | synonymous_variant | 2/2 | ||
GJA4 | XM_017001043.3 | c.132G>A | p.Val44= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJA4 | ENST00000342280.5 | c.132G>A | p.Val44= | synonymous_variant | 2/2 | 1 | NM_002060.3 | P1 | |
SMIM12 | ENST00000426886.1 | c.207+61426C>T | intron_variant, NMD_transcript_variant | 1 | |||||
GJA4 | ENST00000450137.1 | c.132G>A | p.Val44= | synonymous_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.265 AC: 40280AN: 152026Hom.: 6376 Cov.: 32
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GnomAD3 exomes AF: 0.198 AC: 49845AN: 251432Hom.: 5970 AF XY: 0.192 AC XY: 26129AN XY: 135900
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GnomAD4 exome AF: 0.201 AC: 294275AN: 1461720Hom.: 31957 Cov.: 34 AF XY: 0.198 AC XY: 143979AN XY: 727166
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GnomAD4 genome ? AF: 0.265 AC: 40316AN: 152144Hom.: 6388 Cov.: 32 AF XY: 0.263 AC XY: 19586AN XY: 74372
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at