rs10500773

Variant names:

• chr11-13150680-G-A
• rs10500773

Your query was ambiguous. Multiple possible variants found:

• chr11-13150680-G-A
• chr11-13150680-G-C

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 0.423 in 151,730 control chromosomes in the GnomAD database, including 13,826 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 0.42 (13826 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 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: 0.423 AC: 64201 AN: 151612 Hom.: 13830 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.439

Gnomad OTH AF: 0.426

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

GnomAD4 genome AF: 0.423 AC: 64228 AN: 151730 Hom.: 13826 Cov.: 31 AF XY: 0.430 AC XY: 31895 AN XY: 74150

African (AFR) AF: 0.347 AC: 14339 AN: 41328

American (AMR) AF: 0.429 AC: 6531 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3468

East Asian (EAS) AF: 0.566 AC: 2917 AN: 5156

South Asian (SAS) AF: 0.600 AC: 2882 AN: 4804

European-Finnish (FIN) AF: 0.441 AC: 4648 AN: 10530

Middle Eastern (MID) AF: 0.507 AC: 147 AN: 290

European-Non Finnish (NFE) AF: 0.439 AC: 29833 AN: 67920

Other (OTH) AF: 0.426 AC: 895 AN: 2100

Alfa AF: 0.436 Hom.: 12237

Bravo AF: 0.412

Asia WGS AF: 0.581 AC: 2019 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	5.8
DANN	Benign	0.44
PhyloP100		0.066

Splicing

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

Other links and lift over

dbSNP: rs10500773; hg19: chr11-13172227; COSMIC: COSV73321229;