rs10501217

Variant names:

• chr11-40070819-T-C
• rs10501217

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 0.189 in 152,202 control chromosomes in the GnomAD database, including 3,497 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 0.19 (3497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.124
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.275 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: 0.189 AC: 28816 AN: 152084 Hom.: 3495 Cov.: 32

Gnomad AFR AF: 0.0492

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.278

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.189 AC: 28816 AN: 152202 Hom.: 3497 Cov.: 32 AF XY: 0.185 AC XY: 13744 AN XY: 74398

African (AFR) AF: 0.0491 AC: 2041 AN: 41564

American (AMR) AF: 0.195 AC: 2975 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.103 AC: 530 AN: 5162

South Asian (SAS) AF: 0.108 AC: 521 AN: 4820

European-Finnish (FIN) AF: 0.233 AC: 2466 AN: 10602

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.278 AC: 18904 AN: 68002

Other (OTH) AF: 0.189 AC: 399 AN: 2116

Alfa AF: 0.243 Hom.: 8205

Bravo AF: 0.180

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.9
DANN	Benign	0.78
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs10501217; hg19: chr11-40092369;