12-61312496-C-T

Variant names:

• chr12-61312496-C-T
• rs2731402

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.781

Gnomad4 ASJ AF: 0.845

Gnomad4 EAS AF: 0.915

Gnomad4 SAS AF: 0.833

Gnomad4 FIN AF: 0.621

Gnomad4 NFE AF: 0.726

Gnomad4 OTH AF: 0.786

Alfa AF: 0.735 Hom.: 11990

Bravo AF: 0.786

Asia WGS AF: 0.829 AC: 2882 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2731402; hg19: chr12-61706277;