12-62983598-C-T

Position:

• chr12-62983598-C-T

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 0.918 in 152,268 control chromosomes in the GnomAD database, including 64,251 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 0.92 (64251 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.363

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.918 AC: 139723 AN: 152150 Hom.: 64201 Cov.: 32

Gnomad AFR AF: 0.909

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.931

Gnomad ASJ AF: 0.919

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.944

Gnomad FIN AF: 0.921

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.918 AC: 139832 AN: 152268 Hom.: 64251 Cov.: 32 AF XY: 0.919 AC XY: 68372 AN XY: 74438

Gnomad4 AFR AF: 0.909

Gnomad4 AMR AF: 0.931

Gnomad4 ASJ AF: 0.919

Gnomad4 EAS AF: 0.996

Gnomad4 SAS AF: 0.943

Gnomad4 FIN AF: 0.921

Gnomad4 NFE AF: 0.913

Gnomad4 OTH AF: 0.917

Alfa AF: 0.914 Hom.: 58823

Bravo AF: 0.918

Asia WGS AF: 0.963 AC: 3351 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
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: rs699615; hg19: chr12-63377378;