chr7-127442898-A-G

Variant names:

• chr7-127442898-A-G
• rs12666432

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 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

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;