rs11010908

Variant names:

• chr10-36845725-C-T
• rs11010908

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 0.0501 in 152,190 control chromosomes in the GnomAD database, including 256 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 0.050 (256 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.510
• Publications: 1 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 = 0.088 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: 0.0501 AC: 7612 AN: 152072 Hom.: 254 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0375

Gnomad ASJ AF: 0.0804

Gnomad EAS AF: 0.0481

Gnomad SAS AF: 0.0943

Gnomad FIN AF: 0.0503

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0702

Gnomad OTH AF: 0.0521

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

GnomAD4 genome AF: 0.0501 AC: 7623 AN: 152190 Hom.: 256 Cov.: 32 AF XY: 0.0498 AC XY: 3702 AN XY: 74402

African (AFR) AF: 0.0137 AC: 571 AN: 41536

American (AMR) AF: 0.0377 AC: 576 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0804 AC: 279 AN: 3470

East Asian (EAS) AF: 0.0484 AC: 250 AN: 5170

South Asian (SAS) AF: 0.0952 AC: 459 AN: 4822

European-Finnish (FIN) AF: 0.0503 AC: 533 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0702 AC: 4773 AN: 67990

Other (OTH) AF: 0.0535 AC: 113 AN: 2114

Alfa AF: 0.0611 Hom.: 37

Bravo AF: 0.0459

Asia WGS AF: 0.0570 AC: 200 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	3.5
DANN	Benign	0.82
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs11010908; hg19: chr10-37134653;