rs167125

Positions:

• chr11-37851243-C-T

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;