rs12691874

Positions:

• chr2-136122904-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;