rs10837012

Positions:

• chr11-38566720-G-A
• chr11-38566720-G-C
• chr11-38566720-G-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 0.769 in 151,818 control chromosomes in the GnomAD database, including 48,931 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 0.77 (48931 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.284

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.941 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.769 AC: 116653 AN: 151702 Hom.: 48925 Cov.: 31

Gnomad AFR AF: 0.413

Gnomad AMI AF: 0.946

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.947

Gnomad EAS AF: 0.640

Gnomad SAS AF: 0.742

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.769 AC: 116698 AN: 151818 Hom.: 48931 Cov.: 31 AF XY: 0.768 AC XY: 57000 AN XY: 74178

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.824

Gnomad4 ASJ AF: 0.947

Gnomad4 EAS AF: 0.642

Gnomad4 SAS AF: 0.742

Gnomad4 FIN AF: 0.922

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.798

Alfa AF: 0.871 Hom.: 14740

Bravo AF: 0.746

Asia WGS AF: 0.648 AC: 2245 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.8
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10837012; hg19: chr11-38588270;