rs1692141
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_181703.4(GJA5):c.*53G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
Consequence
GJA5
NM_181703.4 3_prime_UTR
NM_181703.4 3_prime_UTR
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.559
Genes affected
GJA5 (HGNC:4279): (gap junction protein alpha 5) This gene is 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 may be associated with atrial fibrillation. Alternatively spliced transcript variants encoding the same isoform have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GJA5 | NM_181703.4 | c.*53G>T | 3_prime_UTR_variant | 2/2 | ENST00000579774.3 | ||
LOC102723321 | XR_922079.4 | n.82-19452C>A | intron_variant, non_coding_transcript_variant | ||||
GJA5 | NM_005266.7 | c.*53G>T | 3_prime_UTR_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJA5 | ENST00000579774.3 | c.*53G>T | 3_prime_UTR_variant | 2/2 | 1 | NM_181703.4 | P1 | ||
ENST00000612401.1 | n.309-294C>A | intron_variant, non_coding_transcript_variant | 5 | ||||||
GJA5 | ENST00000621517.1 | c.*53G>T | 3_prime_UTR_variant | 2/2 | 2 | P1 | |||
ENST00000622634.1 | n.480-245C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 15
GnomAD4 exome
Cov.:
15
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at