rs10504696

Variant names:

• chr8-79148706-G-A
• rs10504696

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.334 in 152,108 control chromosomes in the GnomAD database, including 13,580 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 0.33 (13580 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.138
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50665 AN: 151988 Hom.: 13538 Cov.: 32

Gnomad AFR AF: 0.744

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.305

Gnomad SAS AF: 0.306

Gnomad FIN AF: 0.131

Gnomad MID AF: 0.245

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.301

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

GnomAD4 genome AF: 0.334 AC: 50767 AN: 152108 Hom.: 13580 Cov.: 32 AF XY: 0.331 AC XY: 24611 AN XY: 74376

African (AFR) AF: 0.744 AC: 30877 AN: 41498

American (AMR) AF: 0.235 AC: 3582 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3468

East Asian (EAS) AF: 0.305 AC: 1577 AN: 5168

South Asian (SAS) AF: 0.306 AC: 1479 AN: 4828

European-Finnish (FIN) AF: 0.131 AC: 1386 AN: 10584

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.151 AC: 10235 AN: 67986

Other (OTH) AF: 0.305 AC: 642 AN: 2106

Alfa AF: 0.227 Hom.: 19893

Bravo AF: 0.358

Asia WGS AF: 0.348 AC: 1211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.46
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs10504696; hg19: chr8-80060941;