2-234641677-G-A

Variant names:

• chr2-234641677-G-A
• rs10167927

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 0.737 in 152,158 control chromosomes in the GnomAD database, including 41,648 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 0.74 (41648 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.297
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.866 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: 0.737 AC: 112095 AN: 152040 Hom.: 41612 Cov.: 32

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.779

Gnomad AMR AF: 0.806

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.794

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.711

Gnomad OTH AF: 0.759

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

GnomAD4 genome AF: 0.737 AC: 112186 AN: 152158 Hom.: 41648 Cov.: 32 AF XY: 0.742 AC XY: 55204 AN XY: 74390

African (AFR) AF: 0.707 AC: 29324 AN: 41480

American (AMR) AF: 0.806 AC: 12321 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2757 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4602 AN: 5184

South Asian (SAS) AF: 0.795 AC: 3825 AN: 4814

European-Finnish (FIN) AF: 0.797 AC: 8450 AN: 10602

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.711 AC: 48382 AN: 68006

Other (OTH) AF: 0.761 AC: 1609 AN: 2114

Alfa AF: 0.723 Hom.: 22042

Bravo AF: 0.737

Asia WGS AF: 0.865 AC: 3007 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.36
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs10167927; hg19: chr2-235550321;