12-28948087-A-G

Position:

• chr12-28948087-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 0.565 in 151,618 control chromosomes in the GnomAD database, including 24,695 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 0.57 (24695 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.317

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 (AMR) allele frequency at 95% confidence interval = 0.664 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: 0.565 AC: 85667 AN: 151500 Hom.: 24686 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.582

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.565 AC: 85696 AN: 151618 Hom.: 24695 Cov.: 32 AF XY: 0.572 AC XY: 42376 AN XY: 74046

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.582

Gnomad4 OTH AF: 0.560

Alfa AF: 0.585 Hom.: 4453

Bravo AF: 0.565

Asia WGS AF: 0.558 AC: 1940 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	7.9
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4931122; hg19: chr12-29101020;