rs167125

Variant names:

• chr11-37851243-C-T
• rs167125

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.930

Gnomad4 EAS AF: 0.827

Gnomad4 SAS AF: 0.761

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.904

Gnomad4 OTH AF: 0.772

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs167125; hg19: chr11-37872793;