rs11003831

Variant names:

• chr10-53778715-G-A
• rs11003831

Your query was ambiguous. Multiple possible variants found:

• chr10-53778715-G-A
• chr10-53778715-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 0.463 in 151,782 control chromosomes in the GnomAD database, including 16,917 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 0.46 (16917 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.857 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: 0.463 AC: 70210 AN: 151664 Hom.: 16896 Cov.: 32

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.501

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.878

Gnomad SAS AF: 0.582

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.421

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

GnomAD4 genome AF: 0.463 AC: 70279 AN: 151782 Hom.: 16917 Cov.: 32 AF XY: 0.467 AC XY: 34600 AN XY: 74140

African (AFR) AF: 0.471 AC: 19473 AN: 41368

American (AMR) AF: 0.469 AC: 7153 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1149 AN: 3468

East Asian (EAS) AF: 0.878 AC: 4531 AN: 5158

South Asian (SAS) AF: 0.582 AC: 2804 AN: 4822

European-Finnish (FIN) AF: 0.435 AC: 4584 AN: 10530

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29131 AN: 67868

Other (OTH) AF: 0.428 AC: 903 AN: 2108

Alfa AF: 0.432 Hom.: 17174

Bravo AF: 0.466

Asia WGS AF: 0.697 AC: 2419 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.35
DANN	Benign	0.39
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11003831; hg19: chr10-55538475;