2-32354691-C-T

Variant names:

• chr2-32354691-C-T
• rs12612824

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 151,622 control chromosomes in the GnomAD database, including 8,128 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 (8128 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.641 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: 0.311 AC: 47136 AN: 151504 Hom.: 8124 Cov.: 31

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.239

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.659

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.320

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

GnomAD4 genome AF: 0.311 AC: 47150 AN: 151622 Hom.: 8128 Cov.: 31 AF XY: 0.316 AC XY: 23383 AN XY: 74034

African (AFR) AF: 0.198 AC: 8165 AN: 41296

American (AMR) AF: 0.325 AC: 4944 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1056 AN: 3468

East Asian (EAS) AF: 0.659 AC: 3410 AN: 5174

South Asian (SAS) AF: 0.516 AC: 2470 AN: 4788

European-Finnish (FIN) AF: 0.313 AC: 3282 AN: 10470

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22821 AN: 67930

Other (OTH) AF: 0.325 AC: 683 AN: 2102

Alfa AF: 0.326 Hom.: 32600

Bravo AF: 0.303

Asia WGS AF: 0.556 AC: 1931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	10
DANN	Benign	0.81
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs12612824; hg19: chr2-32579759;