rs10501817

Positions:

• chr11-94961598-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 0.498 in 151,986 control chromosomes in the GnomAD database, including 19,103 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 0.50 (19103 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.25

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.525 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: 0.498 AC: 75609 AN: 151868 Hom.: 19090 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.667

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.530

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.498 AC: 75646 AN: 151986 Hom.: 19103 Cov.: 32 AF XY: 0.495 AC XY: 36765 AN XY: 74290

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.482

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.530

Gnomad4 OTH AF: 0.507

Alfa AF: 0.522 Hom.: 4229

Bravo AF: 0.492

Asia WGS AF: 0.341 AC: 1187 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.0020
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501817; hg19: chr11-94694763;