rs934167

chr2-226727805-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 0.123 in 151,680 control chromosomes in the GnomAD database, including 1,788 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 0.12 (1788 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18561 AN: 151564 Hom.: 1776 Cov.: 31

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.0846

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.0938

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0897

Gnomad NFE AF: 0.0486

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.123 AC: 18619 AN: 151680 Hom.: 1788 Cov.: 31 AF XY: 0.122 AC XY: 9058 AN XY: 74154

Gnomad4 AFR AF: 0.259

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.0938

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0174

Gnomad4 NFE AF: 0.0487

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0876 Hom.: 136

Bravo AF: 0.141

Asia WGS AF: 0.154 AC: 534 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.14
Dann	Benign	0.15

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs934167; hg19: chr2-227592521;