rs10465885
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The XR_922079.4(LOC102723321):n.82-16929T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
LOC102723321
XR_922079.4 intron, non_coding_transcript
XR_922079.4 intron, non_coding_transcript
Scores
1
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.363
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 -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC102723321 | XR_922079.4 | n.82-16929T>A | intron_variant, non_coding_transcript_variant | ||||
GJA5 | NM_005266.7 | c.-33-1361A>T | intron_variant | ||||
GJA5 | NM_181703.4 | upstream_gene_variant | ENST00000579774.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GJA5 | ENST00000430508.1 | c.-33-1361A>T | intron_variant | 2 | |||||
GJA5 | ENST00000621517.1 | c.-33-1361A>T | intron_variant | 2 | P1 | ||||
GJA5 | ENST00000579774.3 | upstream_gene_variant | 1 | NM_181703.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 50Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
50
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
32
Gnomad4 SAS exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at