12-77199799-C-T

Variant names:

• chr12-77199799-C-T
• rs2369599

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 0.781 in 151,880 control chromosomes in the GnomAD database, including 46,803 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 0.78 (46803 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.888 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: 0.781 AC: 118528 AN: 151762 Hom.: 46752 Cov.: 31

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.693

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.814

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.613

Gnomad FIN AF: 0.767

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.738

Gnomad OTH AF: 0.773

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

GnomAD4 genome AF: 0.781 AC: 118636 AN: 151880 Hom.: 46803 Cov.: 31 AF XY: 0.777 AC XY: 57665 AN XY: 74198

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.814

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.612

Gnomad4 FIN AF: 0.767

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.777

Alfa AF: 0.744 Hom.: 65008

Bravo AF: 0.786

Asia WGS AF: 0.724 AC: 2521 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.69
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2369599; hg19: chr12-77593579;