12-61312496-C-T

Variant names:

• chr12-61312496-C-T
• rs2731402

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 0.769 in 151,968 control chromosomes in the GnomAD database, including 45,284 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 0.77 (45284 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.893 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: 0.768 AC: 116682 AN: 151850 Hom.: 45225 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.781

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.833

Gnomad FIN AF: 0.621

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.786

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

GnomAD4 genome AF: 0.769 AC: 116800 AN: 151968 Hom.: 45284 Cov.: 32 AF XY: 0.765 AC XY: 56818 AN XY: 74280

African (AFR) AF: 0.840 AC: 34852 AN: 41504

American (AMR) AF: 0.781 AC: 11925 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2930 AN: 3468

East Asian (EAS) AF: 0.915 AC: 4717 AN: 5158

South Asian (SAS) AF: 0.833 AC: 4019 AN: 4822

European-Finnish (FIN) AF: 0.621 AC: 6554 AN: 10560

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49262 AN: 67882

Other (OTH) AF: 0.786 AC: 1657 AN: 2108

Alfa AF: 0.739 Hom.: 15334

Bravo AF: 0.786

Asia WGS AF: 0.829 AC: 2882 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	0.78
DANN	Benign	0.16
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs2731402; hg19: chr12-61706277;