rs12989936

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;