rs10508401

Variant names:

• chr10-9133746-A-G
• rs10508401

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 0.0261 in 152,250 control chromosomes in the GnomAD database, including 140 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 0.026 (140 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

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 (AMR) allele frequency at 95% confidence interval = 0.0979 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: 0.0260 AC: 3957 AN: 152132 Hom.: 136 Cov.: 32

Gnomad AFR AF: 0.00598

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.00490

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0256

Gnomad OTH AF: 0.0229

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

GnomAD4 genome AF: 0.0261 AC: 3973 AN: 152250 Hom.: 140 Cov.: 32 AF XY: 0.0278 AC XY: 2069 AN XY: 74450

Gnomad4 AFR AF: 0.00597

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.00490

Gnomad4 EAS AF: 0.00290

Gnomad4 SAS AF: 0.0151

Gnomad4 FIN AF: 0.0250

Gnomad4 NFE AF: 0.0256

Gnomad4 OTH AF: 0.0227

Alfa AF: 0.0262 Hom.: 12

Bravo AF: 0.0312

Asia WGS AF: 0.0120 AC: 40 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	6.4
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10508401; hg19: chr10-9175709;