rs12691874

Variant names:

• chr2-136122904-G-A
• rs12691874

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 0.42 in 151,984 control chromosomes in the GnomAD database, including 15,276 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 0.42 (15276 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.539 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: 0.420 AC: 63790 AN: 151866 Hom.: 15273 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.440

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.645

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.420 AC: 63804 AN: 151984 Hom.: 15276 Cov.: 31 AF XY: 0.419 AC XY: 31125 AN XY: 74306

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.309

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.645

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.400

Alfa AF: 0.497 Hom.: 27951

Bravo AF: 0.391

Asia WGS AF: 0.309 AC: 1079 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	0.38
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12691874; hg19: chr2-136880474;