rs11010908

chr10-36845725-C-T

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 0.0501 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

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 = 0.088 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: 0.0501 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

Gnomad4 AFR AF: 0.0137

Gnomad4 AMR AF: 0.0377

Gnomad4 ASJ AF: 0.0804

Gnomad4 EAS AF: 0.0484

Gnomad4 SAS AF: 0.0952

Gnomad4 FIN AF: 0.0503

Gnomad4 NFE AF: 0.0702

Gnomad4 OTH AF: 0.0535

Alfa AF: 0.0625 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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11010908; hg19: chr10-37134653;