chr12-125949716-C-A

Position:

• chr12-125949716-C-A

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 0.0996 in 152,226 control chromosomes in the GnomAD database, including 834 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 0.10 (834 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.176

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 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: 0.0995 AC: 15139 AN: 152108 Hom.: 830 Cov.: 32

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.190

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.0769

Gnomad EAS AF: 0.0703

Gnomad SAS AF: 0.0757

Gnomad FIN AF: 0.0335

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0878

Gnomad OTH AF: 0.0990

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

GnomAD4 genome AF: 0.0996 AC: 15166 AN: 152226 Hom.: 834 Cov.: 32 AF XY: 0.0969 AC XY: 7215 AN XY: 74430

Gnomad4 AFR AF: 0.143

Gnomad4 AMR AF: 0.0974

Gnomad4 ASJ AF: 0.0769

Gnomad4 EAS AF: 0.0705

Gnomad4 SAS AF: 0.0757

Gnomad4 FIN AF: 0.0335

Gnomad4 NFE AF: 0.0878

Gnomad4 OTH AF: 0.0980

Alfa AF: 0.0567 Hom.: 73

Bravo AF: 0.107

Asia WGS AF: 0.0800 AC: 277 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.52
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs225553; hg19: chr12-126434262;