rs12671332

Variant names:

• chr7-12175936-T-C
• rs12671332

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 0.221 in 151,636 control chromosomes in the GnomAD database, including 4,370 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 0.22 (4370 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 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: 0.221 AC: 33486 AN: 151518 Hom.: 4365 Cov.: 31

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.237

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.221 AC: 33501 AN: 151636 Hom.: 4370 Cov.: 31 AF XY: 0.227 AC XY: 16839 AN XY: 74090

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.359

Gnomad4 ASJ AF: 0.237

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.226

Alfa AF: 0.240 Hom.: 2054

Bravo AF: 0.226

Asia WGS AF: 0.378 AC: 1314 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	0.35
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12671332; hg19: chr7-12215562;