chr1-147909431-A-G

Position:

• chr1-147909431-A-G

Variant summary

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

The XM_011509417.3(GJA8):​c.1280+196A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,086 control chromosomes in the GnomAD database, including 6,293 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 0.17 (6293 hom., cov: 32)
• Consequence: GJA8 XM_011509417.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49

Genes affected

GJA8 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GJA8	XM_011509417.3	c.1280+196A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.165 AC: 25094 AN: 151968 Hom.: 6250 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0581

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.0182

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.00425

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.166 AC: 25194 AN: 152086 Hom.: 6293 Cov.: 32 AF XY: 0.163 AC XY: 12149 AN XY: 74360

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.0579

Gnomad4 ASJ AF: 0.0156

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.0176

Gnomad4 FIN AF: 0.0440

Gnomad4 NFE AF: 0.00425

Gnomad4 OTH AF: 0.117

Alfa AF: 0.0357 Hom.: 1099

Bravo AF: 0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.0020

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2132397; hg19: chr1-147381558;