12-117993522-T-C

Variant names:

• chr12-117993522-T-C
• rs7295696

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 0.418 in 151,876 control chromosomes in the GnomAD database, including 13,530 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 0.42 (13530 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63431 AN: 151756 Hom.: 13527 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.413

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.480

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.455

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

GnomAD4 genome AF: 0.418 AC: 63467 AN: 151876 Hom.: 13530 Cov.: 31 AF XY: 0.414 AC XY: 30745 AN XY: 74224

African (AFR) AF: 0.360 AC: 14919 AN: 41406

American (AMR) AF: 0.378 AC: 5754 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1668 AN: 3464

East Asian (EAS) AF: 0.412 AC: 2126 AN: 5166

South Asian (SAS) AF: 0.295 AC: 1424 AN: 4820

European-Finnish (FIN) AF: 0.480 AC: 5059 AN: 10544

Middle Eastern (MID) AF: 0.466 AC: 136 AN: 292

European-Non Finnish (NFE) AF: 0.457 AC: 31058 AN: 67924

Other (OTH) AF: 0.450 AC: 949 AN: 2108

Alfa AF: 0.439 Hom.: 49590

Bravo AF: 0.412

Asia WGS AF: 0.345 AC: 1198 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	3.9
DANN	Benign	0.55
PhyloP100		0.083

Splicing

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

Other links and lift over

dbSNP: rs7295696; hg19: chr12-118431327; COSMIC: COSV107182535;