rs10831990

Variant names:

• chr11-13175769-T-C
• rs10831990

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The variant allele was found at a frequency of 0.222 in 151,930 control chromosomes in the GnomAD database, including 4,878 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 0.22 (4878 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.31
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.16).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.223 AC: 33792 AN: 151812 Hom.: 4880 Cov.: 31

Gnomad AFR AF: 0.0581

Gnomad AMI AF: 0.222

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.524

Gnomad SAS AF: 0.369

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.278

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.222 AC: 33798 AN: 151930 Hom.: 4878 Cov.: 31 AF XY: 0.229 AC XY: 16988 AN XY: 74236

African (AFR) AF: 0.0580 AC: 2405 AN: 41480

American (AMR) AF: 0.182 AC: 2781 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.355 AC: 1228 AN: 3458

East Asian (EAS) AF: 0.523 AC: 2698 AN: 5156

South Asian (SAS) AF: 0.371 AC: 1777 AN: 4790

European-Finnish (FIN) AF: 0.344 AC: 3612 AN: 10514

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18542 AN: 67940

Other (OTH) AF: 0.223 AC: 472 AN: 2114

Alfa AF: 0.258 Hom.: 9459

Bravo AF: 0.204

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.16
CADD	Benign	22
DANN	Benign	0.64
PhyloP100		3.3

Splicing

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

Other links and lift over

dbSNP: rs10831990; hg19: chr11-13197316;