12-124927460-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.718 in 152,160 control chromosomes in the GnomAD database, including 40,544 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 0.72 (40544 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.79

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.782 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.718 AC: 109180 AN: 152042 Hom.: 40523 Cov.: 34

Gnomad AFR AF: 0.698

Gnomad AMI AF: 0.813

Gnomad AMR AF: 0.642

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.788

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.718 AC: 109247 AN: 152160 Hom.: 40544 Cov.: 34 AF XY: 0.708 AC XY: 52644 AN XY: 74380

Gnomad4 AFR AF: 0.698

Gnomad4 AMR AF: 0.641

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.780

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.788

Gnomad4 OTH AF: 0.736

Alfa AF: 0.781 Hom.: 70219

Bravo AF: 0.711

Asia WGS AF: 0.462 AC: 1608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	0.036
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10846771; hg19: chr12-125412006;