rs10505137

Positions:

• chr8-110129380-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.108

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.0733

Gnomad4 SAS AF: 0.0786

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.155

Gnomad4 OTH AF: 0.139

Alfa AF: 0.151 Hom.: 794

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505137; hg19: chr8-111141609;