rs934167

Variant names:

• chr2-226727805-C-T
• rs934167

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 0.123 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
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.255 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: 0.122 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

African (AFR) AF: 0.259 AC: 10682 AN: 41282

American (AMR) AF: 0.142 AC: 2159 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.0938 AC: 325 AN: 3466

East Asian (EAS) AF: 0.188 AC: 970 AN: 5156

South Asian (SAS) AF: 0.140 AC: 674 AN: 4810

European-Finnish (FIN) AF: 0.0174 AC: 183 AN: 10500

Middle Eastern (MID) AF: 0.0862 AC: 25 AN: 290

European-Non Finnish (NFE) AF: 0.0487 AC: 3307 AN: 67962

Other (OTH) AF: 0.103 AC: 217 AN: 2098

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
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs934167; hg19: chr2-227592521;