rs10505364

Variant names:

• chr8-119496864-A-G
• rs10505364

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 0.366 in 152,042 control chromosomes in the GnomAD database, including 11,218 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 0.37 (11218 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.565 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: 0.366 AC: 55652 AN: 151926 Hom.: 11219 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.415

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.584

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.366 AC: 55662 AN: 152042 Hom.: 11218 Cov.: 32 AF XY: 0.372 AC XY: 27640 AN XY: 74304

African (AFR) AF: 0.196 AC: 8145 AN: 41468

American (AMR) AF: 0.427 AC: 6512 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.415 AC: 1441 AN: 3470

East Asian (EAS) AF: 0.298 AC: 1540 AN: 5160

South Asian (SAS) AF: 0.583 AC: 2808 AN: 4816

European-Finnish (FIN) AF: 0.473 AC: 4994 AN: 10560

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28813 AN: 67980

Other (OTH) AF: 0.377 AC: 798 AN: 2116

Alfa AF: 0.407 Hom.: 7667

Bravo AF: 0.349

Asia WGS AF: 0.478 AC: 1660 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	1.9
DANN	Benign	0.46
PhyloP100		-0.28

Splicing

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

Other links and lift over

dbSNP: rs10505364; hg19: chr8-120509104; COSMIC: COSV107189734;