2-232453514-T-C

Variant names:

• chr2-232453514-T-C
• rs3762521

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 0.283 in 152,132 control chromosomes in the GnomAD database, including 6,367 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 0.28 (6367 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.452 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.282 AC: 42928 AN: 152012 Hom.: 6347 Cov.: 32

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.271

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

GnomAD4 genome AF: 0.283 AC: 42982 AN: 152132 Hom.: 6367 Cov.: 32 AF XY: 0.288 AC XY: 21422 AN XY: 74366

African (AFR) AF: 0.228 AC: 9455 AN: 41518

American (AMR) AF: 0.357 AC: 5457 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1052 AN: 3470

East Asian (EAS) AF: 0.467 AC: 2415 AN: 5170

South Asian (SAS) AF: 0.381 AC: 1838 AN: 4820

European-Finnish (FIN) AF: 0.318 AC: 3359 AN: 10558

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.273 AC: 18577 AN: 67998

Other (OTH) AF: 0.274 AC: 579 AN: 2112

Alfa AF: 0.279 Hom.: 773

Bravo AF: 0.284

Asia WGS AF: 0.440 AC: 1524 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
CADD	Benign	2.8
DANN	Benign	0.61
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs3762521; hg19: chr2-233318224;