12-62983598-C-T

Variant names:

• chr12-62983598-C-T
• rs699615

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;