chr7-12175936-T-C

Variant names:

• chr7-12175936-T-C
• rs12671332

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 0.221 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
• Publications: 5 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 (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.104 AC: 4290 AN: 41296

American (AMR) AF: 0.359 AC: 5463 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.237 AC: 822 AN: 3464

East Asian (EAS) AF: 0.472 AC: 2435 AN: 5160

South Asian (SAS) AF: 0.351 AC: 1685 AN: 4802

European-Finnish (FIN) AF: 0.213 AC: 2231 AN: 10456

Middle Eastern (MID) AF: 0.260 AC: 76 AN: 292

European-Non Finnish (NFE) AF: 0.234 AC: 15880 AN: 67936

Other (OTH) AF: 0.226 AC: 474 AN: 2102

Alfa AF: 0.238 Hom.: 2283

Bravo AF: 0.226

Asia WGS AF: 0.378 AC: 1314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.35
DANN	Benign	0.65
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12671332; hg19: chr7-12215562;