chr12-114905687-C-T

Variant names:

• chr12-114905687-C-T
• rs7963771

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 0.334 in 151,942 control chromosomes in the GnomAD database, including 8,813 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 (8813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.137
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.404 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: 0.334 AC: 50755 AN: 151822 Hom.: 8797 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.206

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.443

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.516

Gnomad NFE AF: 0.328

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.334 AC: 50813 AN: 151942 Hom.: 8813 Cov.: 32 AF XY: 0.332 AC XY: 24622 AN XY: 74262

African (AFR) AF: 0.356 AC: 14739 AN: 41394

American (AMR) AF: 0.412 AC: 6291 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.443 AC: 1533 AN: 3464

East Asian (EAS) AF: 0.124 AC: 640 AN: 5158

South Asian (SAS) AF: 0.366 AC: 1759 AN: 4808

European-Finnish (FIN) AF: 0.230 AC: 2437 AN: 10578

Middle Eastern (MID) AF: 0.510 AC: 150 AN: 294

European-Non Finnish (NFE) AF: 0.328 AC: 22296 AN: 67962

Other (OTH) AF: 0.369 AC: 780 AN: 2112

Alfa AF: 0.325 Hom.: 8140

Bravo AF: 0.349

Asia WGS AF: 0.242 AC: 842 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.3
DANN	Benign	0.23
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs7963771; hg19: chr12-115343492;