12-66187806-C-T

Variant names:

• chr12-66187806-C-T
• rs1732888

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.76 in 152,144 control chromosomes in the GnomAD database, including 44,780 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 0.76 (44780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.893 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: 0.760 AC: 115471 AN: 152026 Hom.: 44724 Cov.: 32

Gnomad AFR AF: 0.900

Gnomad AMI AF: 0.814

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.884

Gnomad SAS AF: 0.759

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.760 AC: 115583 AN: 152144 Hom.: 44780 Cov.: 32 AF XY: 0.758 AC XY: 56375 AN XY: 74378

African (AFR) AF: 0.900 AC: 37386 AN: 41522

American (AMR) AF: 0.622 AC: 9512 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3470

East Asian (EAS) AF: 0.884 AC: 4572 AN: 5172

South Asian (SAS) AF: 0.759 AC: 3668 AN: 4830

European-Finnish (FIN) AF: 0.671 AC: 7089 AN: 10566

Middle Eastern (MID) AF: 0.793 AC: 233 AN: 294

European-Non Finnish (NFE) AF: 0.708 AC: 48143 AN: 67984

Other (OTH) AF: 0.733 AC: 1549 AN: 2114

Alfa AF: 0.740 Hom.: 10398

Bravo AF: 0.760

Asia WGS AF: 0.806 AC: 2804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.4
DANN	Benign	0.65
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1732888; hg19: chr12-66581586;