rs10505137

Variant names:

• chr8-110129380-G-A
• rs10505137

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 0.141 in 151,270 control chromosomes in the GnomAD database, including 1,617 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 0.14 (1617 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.592
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.152 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: 0.141 AC: 21370 AN: 151192 Hom.: 1621 Cov.: 31

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0736

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.0729

Gnomad SAS AF: 0.0790

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.154

Gnomad OTH AF: 0.140

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

GnomAD4 genome AF: 0.141 AC: 21371 AN: 151270 Hom.: 1617 Cov.: 31 AF XY: 0.143 AC XY: 10546 AN XY: 73912

African (AFR) AF: 0.123 AC: 5075 AN: 41314

American (AMR) AF: 0.108 AC: 1635 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 570 AN: 3464

East Asian (EAS) AF: 0.0733 AC: 377 AN: 5146

South Asian (SAS) AF: 0.0786 AC: 377 AN: 4794

European-Finnish (FIN) AF: 0.237 AC: 2478 AN: 10476

Middle Eastern (MID) AF: 0.191 AC: 55 AN: 288

European-Non Finnish (NFE) AF: 0.155 AC: 10445 AN: 67604

Other (OTH) AF: 0.139 AC: 292 AN: 2094

Alfa AF: 0.150 Hom.: 890

Bravo AF: 0.132

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.37
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10505137; hg19: chr8-111141609;