rs12989936

Variant names:

• chr2-32043517-T-C
• rs12989936

Your query was ambiguous. Multiple possible variants found:

• chr2-32043517-T-C
• chr2-32043517-T-G

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 0.445 in 151,664 control chromosomes in the GnomAD database, including 15,328 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 0.44 (15328 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.628 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: 0.445 AC: 67398 AN: 151548 Hom.: 15310 Cov.: 31

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.389

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.512

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.445 AC: 67461 AN: 151664 Hom.: 15328 Cov.: 31 AF XY: 0.445 AC XY: 32987 AN XY: 74102

African (AFR) AF: 0.490 AC: 20252 AN: 41348

American (AMR) AF: 0.432 AC: 6570 AN: 15198

Ashkenazi Jewish (ASJ) AF: 0.512 AC: 1773 AN: 3466

East Asian (EAS) AF: 0.646 AC: 3325 AN: 5146

South Asian (SAS) AF: 0.557 AC: 2682 AN: 4814

European-Finnish (FIN) AF: 0.372 AC: 3899 AN: 10486

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.405 AC: 27519 AN: 67908

Other (OTH) AF: 0.442 AC: 930 AN: 2104

Alfa AF: 0.424 Hom.: 6059

Bravo AF: 0.451

Asia WGS AF: 0.631 AC: 2190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.51
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs12989936; hg19: chr2-32268586;