rs10510911

Positions:

• chr3-63717965-C-G
• chr3-63717965-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 0.387 in 151,988 control chromosomes in the GnomAD database, including 11,413 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 0.39 (11413 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.397 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: 0.386 AC: 58689 AN: 151870 Hom.: 11391 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.453

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.331

Gnomad NFE AF: 0.398

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.387 AC: 58762 AN: 151988 Hom.: 11413 Cov.: 32 AF XY: 0.385 AC XY: 28613 AN XY: 74292

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.359

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.398

Gnomad4 OTH AF: 0.396

Alfa AF: 0.387 Hom.: 1609

Bravo AF: 0.388

Asia WGS AF: 0.351 AC: 1224 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.5
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10510911; hg19: chr3-63703641;