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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.490

Gnomad4 AMR AF: 0.432

Gnomad4 ASJ AF: 0.512

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.372

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.442

Alfa AF: 0.423 Hom.: 4900

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12989936; hg19: chr2-32268586;