1-147760632-T-C

Variant names:

• chr1-147760632-T-C
• rs10465885
• NM_005266.7:c.-33-1361A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_005266.7(GJA5):​c.-33-1361A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 152,068 control chromosomes in the GnomAD database, including 15,930 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 0.46 (15920 hom., cov: 32)
  • Exomes 𝑓: 0.56 (10 hom.)
• Consequence: GJA5 NM_005266.7 intron
• 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]

LOC102723321 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GJA5	NM_005266.7	c.-33-1361A>G		intron_variant	Intron 1 of 1		NP_005257.2
LOC102723321	XR_922079.4	n.82-16929T>C		intron_variant	Intron 1 of 2
GJA5	NM_181703.4	c.-167A>G		upstream_gene_variant		ENST00000579774.3	NP_859054.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GJA5	ENST00000621517.1	c.-33-1361A>G		intron_variant	Intron 1 of 1	2		ENSP00000484552.1
GJA5	ENST00000430508.1	c.-33-1361A>G		intron_variant	Intron 1 of 1	2		ENSP00000407645.1
GJA5	ENST00000579774.3	c.-167A>G		upstream_gene_variant		1	NM_181703.4	ENSP00000463851.1

Frequencies

GnomAD3 genomes AF: 0.457 AC: 69381 AN: 151900 Hom.: 15874 Cov.: 32

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.547

Gnomad AMR AF: 0.536

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.549

Gnomad SAS AF: 0.462

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.560 AC: 28 AN: 50 Hom.: 10 Cov.: 0 AF XY: 0.563 AC XY: 18 AN XY: 32

Gnomad4 SAS exome AF: 0.500

Gnomad4 NFE exome AF: 0.548

Gnomad4 OTH exome AF: 0.667

GnomAD4 genome AF: 0.457 AC: 69477 AN: 152018 Hom.: 15920 Cov.: 32 AF XY: 0.457 AC XY: 33991 AN XY: 74334

Gnomad4 AFR AF: 0.387

Gnomad4 AMR AF: 0.536

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.550

Gnomad4 SAS AF: 0.462

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.487

Alfa AF: 0.471 Hom.: 18265

Bravo AF: 0.464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10465885; hg19: chr1-147232740;