2-231423438-G-A

Variant names:

• chr2-231423438-G-A
• rs2034413

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 0.311 in 152,138 control chromosomes in the GnomAD database, including 7,729 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 0.31 (7729 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.546
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47276 AN: 152020 Hom.: 7729 Cov.: 33

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.271

Gnomad ASJ AF: 0.372

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.368

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.316

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.311 AC: 47297 AN: 152138 Hom.: 7729 Cov.: 33 AF XY: 0.314 AC XY: 23372 AN XY: 74354

African (AFR) AF: 0.254 AC: 10534 AN: 41484

American (AMR) AF: 0.270 AC: 4133 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.372 AC: 1293 AN: 3472

East Asian (EAS) AF: 0.609 AC: 3150 AN: 5174

South Asian (SAS) AF: 0.351 AC: 1694 AN: 4828

European-Finnish (FIN) AF: 0.368 AC: 3893 AN: 10576

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.316 AC: 21478 AN: 67994

Other (OTH) AF: 0.328 AC: 694 AN: 2116

Alfa AF: 0.299 Hom.: 1306

Bravo AF: 0.302

Asia WGS AF: 0.437 AC: 1521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.1
DANN	Benign	0.94
PhyloP100		0.55

Splicing

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

Other links and lift over

dbSNP: rs2034413; hg19: chr2-232288149;