rs10901513

Variant names:

• chr10-126011367-T-C
• rs10901513

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 0.348 in 152,138 control chromosomes in the GnomAD database, including 9,638 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 0.35 (9638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00700
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.435 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: 0.348 AC: 52949 AN: 152020 Hom.: 9626 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.416

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.449

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.334

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.365

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

GnomAD4 genome AF: 0.348 AC: 52984 AN: 152138 Hom.: 9638 Cov.: 32 AF XY: 0.345 AC XY: 25667 AN XY: 74364

African (AFR) AF: 0.254 AC: 10527 AN: 41512

American (AMR) AF: 0.298 AC: 4546 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1635 AN: 3472

East Asian (EAS) AF: 0.330 AC: 1704 AN: 5170

South Asian (SAS) AF: 0.451 AC: 2171 AN: 4818

European-Finnish (FIN) AF: 0.332 AC: 3514 AN: 10572

Middle Eastern (MID) AF: 0.332 AC: 97 AN: 292

European-Non Finnish (NFE) AF: 0.406 AC: 27633 AN: 68006

Other (OTH) AF: 0.369 AC: 778 AN: 2110

Alfa AF: 0.382 Hom.: 17941

Bravo AF: 0.339

Asia WGS AF: 0.380 AC: 1320 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	1.3
DANN	Benign	0.46
PhyloP100		0.0070

Splicing

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

Other links and lift over

dbSNP: rs10901513; hg19: chr10-127699936;