rs13432762

Variant names:

• chr2-142142123-C-T
• rs13432762

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 0.0731 in 152,028 control chromosomes in the GnomAD database, including 775 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 0.073 (775 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.174
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.171 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: 0.0729 AC: 11079 AN: 151910 Hom.: 771 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.00923

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.0964

Gnomad FIN AF: 0.0163

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.0621

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

GnomAD4 genome AF: 0.0731 AC: 11106 AN: 152028 Hom.: 775 Cov.: 32 AF XY: 0.0723 AC XY: 5371 AN XY: 74318

African (AFR) AF: 0.175 AC: 7235 AN: 41418

American (AMR) AF: 0.0747 AC: 1141 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.00923 AC: 32 AN: 3468

East Asian (EAS) AF: 0.0397 AC: 206 AN: 5184

South Asian (SAS) AF: 0.0956 AC: 460 AN: 4810

European-Finnish (FIN) AF: 0.0163 AC: 172 AN: 10574

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0253 AC: 1720 AN: 67984

Other (OTH) AF: 0.0615 AC: 130 AN: 2114

Alfa AF: 0.0561 Hom.: 76

Bravo AF: 0.0805

Asia WGS AF: 0.0710 AC: 246 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	14
DANN	Benign	0.71
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs13432762; hg19: chr2-142899692;