rs10831990

Variant names:

• chr11-13175769-T-C
• rs10831990

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.223 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

Gnomad4 AFR AF: 0.0580

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.523

Gnomad4 SAS AF: 0.371

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.223

Alfa AF: 0.265 Hom.: 7301

Bravo AF: 0.204

Asia WGS AF: 0.385 AC: 1339 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10831990; hg19: chr11-13197316;