rs12666432

Positions:

• chr7-127442898-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 0.328 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.0910

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.267

Gnomad4 EAS AF: 0.729

Gnomad4 SAS AF: 0.407

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.328

Alfa AF: 0.372 Hom.: 1919

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12666432; hg19: chr7-127082952;