rs10500773

Positions:

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

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 0.423 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.489

Gnomad4 EAS AF: 0.566

Gnomad4 SAS AF: 0.600

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.439

Gnomad4 OTH AF: 0.426

Alfa AF: 0.438 Hom.: 10476

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

Splicing

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

Publications

LitVar

Other links and lift over

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