2-231423350-C-G

Variant names:

• chr2-231423350-C-G
• rs2034412

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 0.299 in 152,124 control chromosomes in the GnomAD database, including 7,308 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 0.30 (7308 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.592 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: 0.299 AC: 45456 AN: 152006 Hom.: 7306 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.345

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.370

Gnomad EAS AF: 0.609

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.367

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.299 AC: 45471 AN: 152124 Hom.: 7308 Cov.: 32 AF XY: 0.303 AC XY: 22522 AN XY: 74350

African (AFR) AF: 0.209 AC: 8690 AN: 41506

American (AMR) AF: 0.266 AC: 4073 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.370 AC: 1284 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3141 AN: 5154

South Asian (SAS) AF: 0.351 AC: 1694 AN: 4824

European-Finnish (FIN) AF: 0.367 AC: 3883 AN: 10572

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

European-Non Finnish (NFE) AF: 0.318 AC: 21602 AN: 67988

Other (OTH) AF: 0.320 AC: 677 AN: 2114

Alfa AF: 0.167 Hom.: 310

Bravo AF: 0.287

Asia WGS AF: 0.435 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.72
DANN	Benign	0.31
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs2034412; hg19: chr2-232288061;