rs12666432

Variant names:

• chr7-127442898-A-G
• rs12666432

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 0.328 in 152,120 control chromosomes in the GnomAD database, including 10,291 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 0.33 (10291 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.71 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: 0.328 AC: 49830 AN: 152002 Hom.: 10279 Cov.: 32

Gnomad AFR AF: 0.0911

Gnomad AMI AF: 0.401

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.267

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.406

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.328 AC: 49842 AN: 152120 Hom.: 10291 Cov.: 32 AF XY: 0.336 AC XY: 25005 AN XY: 74358

African (AFR) AF: 0.0910 AC: 3777 AN: 41520

American (AMR) AF: 0.377 AC: 5758 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.267 AC: 926 AN: 3470

East Asian (EAS) AF: 0.729 AC: 3766 AN: 5166

South Asian (SAS) AF: 0.407 AC: 1960 AN: 4812

European-Finnish (FIN) AF: 0.469 AC: 4959 AN: 10572

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.406 AC: 27575 AN: 67976

Other (OTH) AF: 0.328 AC: 693 AN: 2114

Alfa AF: 0.380 Hom.: 4084

Bravo AF: 0.311

Asia WGS AF: 0.520 AC: 1803 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs12666432; hg19: chr7-127082952;