rs1732887

chr12-66187836-G-Achr12-66187836-G-C

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 0.75 in 152,094 control chromosomes in the GnomAD database, including 43,528 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 0.75 (43528 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.386

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.750 AC: 114027 AN: 151976 Hom.: 43482 Cov.: 31

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.815

Gnomad AMR AF: 0.619

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.732

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

GnomAD4 genome AF: 0.750 AC: 114129 AN: 152094 Hom.: 43528 Cov.: 31 AF XY: 0.749 AC XY: 55702 AN XY: 74350

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.618

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.884

Gnomad4 SAS AF: 0.759

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.731

Alfa AF: 0.709 Hom.: 6776

Bravo AF: 0.749

Asia WGS AF: 0.805 AC: 2800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.4
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1732887; hg19: chr12-66581616;