2-31298423-G-A

Variant names:

• chr2-31298423-G-A
• rs604127

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 0.859 in 152,248 control chromosomes in the GnomAD database, including 56,365 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 0.86 (56365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0270
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.859 AC: 130726 AN: 152130 Hom.: 56309 Cov.: 32

Gnomad AFR AF: 0.884

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.980

Gnomad SAS AF: 0.854

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.859 AC: 130840 AN: 152248 Hom.: 56365 Cov.: 32 AF XY: 0.861 AC XY: 64102 AN XY: 74458

African (AFR) AF: 0.884 AC: 36723 AN: 41548

American (AMR) AF: 0.865 AC: 13238 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2705 AN: 3466

East Asian (EAS) AF: 0.980 AC: 5071 AN: 5176

South Asian (SAS) AF: 0.855 AC: 4113 AN: 4812

European-Finnish (FIN) AF: 0.873 AC: 9269 AN: 10612

Middle Eastern (MID) AF: 0.815 AC: 238 AN: 292

European-Non Finnish (NFE) AF: 0.837 AC: 56943 AN: 68016

Other (OTH) AF: 0.860 AC: 1819 AN: 2116

Alfa AF: 0.841 Hom.: 108161

Bravo AF: 0.861

Asia WGS AF: 0.918 AC: 3192 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.46
DANN	Benign	0.11
PhyloP100		-0.027

Splicing

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

Other links and lift over

dbSNP: rs604127; hg19: chr2-31521289;