12-27974006-A-G

Position:

• chr12-27974006-A-G

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 0.623 in 151,706 control chromosomes in the GnomAD database, including 31,748 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 0.62 (31748 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.797

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.879 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: 0.623 AC: 94418 AN: 151588 Hom.: 31695 Cov.: 29

Gnomad AFR AF: 0.887

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.473

Gnomad SAS AF: 0.505

Gnomad FIN AF: 0.547

Gnomad MID AF: 0.623

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.564

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

GnomAD4 genome AF: 0.623 AC: 94527 AN: 151706 Hom.: 31748 Cov.: 29 AF XY: 0.616 AC XY: 45647 AN XY: 74104

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.429

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.472

Gnomad4 SAS AF: 0.506

Gnomad4 FIN AF: 0.547

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.564

Alfa AF: 0.543 Hom.: 31821

Bravo AF: 0.623

Asia WGS AF: 0.506 AC: 1762 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.41
DANN	Benign	0.19

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1268693; hg19: chr12-28126939;