rs12467660

Variant names:

• chr2-191166924-A-C
• rs12467660

Your query was ambiguous. Multiple possible variants found:

• chr2-191166924-A-C
• chr2-191166924-A-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 0.774 in 152,146 control chromosomes in the GnomAD database, including 47,604 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 0.77 (47604 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.586

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.875 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: 0.774 AC: 117671 AN: 152028 Hom.: 47584 Cov.: 31

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.935

Gnomad EAS AF: 0.649

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.937

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.791

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

GnomAD4 genome AF: 0.774 AC: 117733 AN: 152146 Hom.: 47604 Cov.: 31 AF XY: 0.781 AC XY: 58151 AN XY: 74422

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.858

Gnomad4 ASJ AF: 0.935

Gnomad4 EAS AF: 0.650

Gnomad4 SAS AF: 0.821

Gnomad4 FIN AF: 0.937

Gnomad4 NFE AF: 0.881

Gnomad4 OTH AF: 0.789

Alfa AF: 0.822 Hom.: 9814

Bravo AF: 0.755

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.5
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12467660; hg19: chr2-192031650;