rs10508622

chr10-20409341-T-Achr10-20409341-T-C

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 0.149 in 152,186 control chromosomes in the GnomAD database, including 1,842 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 0.15 (1842 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.181 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.149 AC: 22703 AN: 152068 Hom.: 1833 Cov.: 32

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.150

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.149 AC: 22735 AN: 152186 Hom.: 1842 Cov.: 32 AF XY: 0.151 AC XY: 11273 AN XY: 74416

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.152

Alfa AF: 0.0866 Hom.: 128

Bravo AF: 0.139

Asia WGS AF: 0.148 AC: 515 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.14
Dann	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508622; hg19: chr10-20698270;