chr10-20409589-C-T

Variant names:

• chr10-20409589-C-T
• rs10508623

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 151,952 control chromosomes in the GnomAD database, including 1,841 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 (1841 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 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: 0.149 AC: 22600 AN: 151834 Hom.: 1832 Cov.: 32

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.172

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.149 AC: 22632 AN: 151952 Hom.: 1841 Cov.: 32 AF XY: 0.151 AC XY: 11203 AN XY: 74238

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.107

Gnomad4 ASJ AF: 0.172

Gnomad4 EAS AF: 0.105

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.173

Gnomad4 NFE AF: 0.180

Gnomad4 OTH AF: 0.152

Alfa AF: 0.164 Hom.: 2849

Bravo AF: 0.139

Asia WGS AF: 0.147 AC: 513 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508623; hg19: chr10-20698518;