rs10830237

Variant names:

• chr11-89168976-C-T
• rs10830237

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 0.517 in 151,944 control chromosomes in the GnomAD database, including 21,390 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 0.52 (21390 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.90
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78602 AN: 151826 Hom.: 21393 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.735

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.674

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.517 AC: 78627 AN: 151944 Hom.: 21390 Cov.: 33 AF XY: 0.520 AC XY: 38601 AN XY: 74244

African (AFR) AF: 0.336 AC: 13908 AN: 41448

American (AMR) AF: 0.575 AC: 8774 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.674 AC: 2340 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3443 AN: 5142

South Asian (SAS) AF: 0.663 AC: 3199 AN: 4822

European-Finnish (FIN) AF: 0.519 AC: 5478 AN: 10558

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39443 AN: 67938

Other (OTH) AF: 0.568 AC: 1192 AN: 2100

Alfa AF: 0.502 Hom.: 2929

Bravo AF: 0.517

Asia WGS AF: 0.627 AC: 2181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0090
DANN	Benign	0.62
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs10830237; hg19: chr11-88902144;