12-115940325-C-T

Variant names:

• chr12-115940325-C-T
• rs10774841

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 0.553 in 152,028 control chromosomes in the GnomAD database, including 24,749 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 0.55 (24749 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.737
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.761 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: 0.553 AC: 84021 AN: 151910 Hom.: 24715 Cov.: 31

Gnomad AFR AF: 0.768

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.458

Gnomad OTH AF: 0.537

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

GnomAD4 genome AF: 0.553 AC: 84110 AN: 152028 Hom.: 24749 Cov.: 31 AF XY: 0.553 AC XY: 41108 AN XY: 74308

African (AFR) AF: 0.768 AC: 31871 AN: 41502

American (AMR) AF: 0.495 AC: 7557 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2172 AN: 5170

South Asian (SAS) AF: 0.366 AC: 1760 AN: 4808

European-Finnish (FIN) AF: 0.624 AC: 6578 AN: 10546

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.458 AC: 31123 AN: 67946

Other (OTH) AF: 0.537 AC: 1132 AN: 2108

Alfa AF: 0.489 Hom.: 50523

Bravo AF: 0.560

Asia WGS AF: 0.391 AC: 1358 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	0.14
DANN	Benign	0.34
PhyloP100		-0.74

Splicing

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

Other links and lift over

dbSNP: rs10774841; hg19: chr12-116378130;