rs167125

Variant names:

• chr11-37851243-C-T
• rs167125

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 0.726 in 152,134 control chromosomes in the GnomAD database, including 44,725 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 0.73 (44725 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.898 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: 0.726 AC: 110426 AN: 152016 Hom.: 44734 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.966

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.930

Gnomad EAS AF: 0.828

Gnomad SAS AF: 0.762

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.904

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.726 AC: 110432 AN: 152134 Hom.: 44725 Cov.: 32 AF XY: 0.726 AC XY: 54010 AN XY: 74374

African (AFR) AF: 0.334 AC: 13863 AN: 41464

American (AMR) AF: 0.764 AC: 11673 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.930 AC: 3225 AN: 3468

East Asian (EAS) AF: 0.827 AC: 4278 AN: 5174

South Asian (SAS) AF: 0.761 AC: 3670 AN: 4820

European-Finnish (FIN) AF: 0.894 AC: 9490 AN: 10610

Middle Eastern (MID) AF: 0.854 AC: 251 AN: 294

European-Non Finnish (NFE) AF: 0.904 AC: 61472 AN: 68012

Other (OTH) AF: 0.772 AC: 1629 AN: 2110

Alfa AF: 0.740 Hom.: 6592

Bravo AF: 0.701

Asia WGS AF: 0.746 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.8
DANN	Benign	0.56
PhyloP100		0.057

Splicing

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

Other links and lift over

dbSNP: rs167125; hg19: chr11-37872793;