12-28002147-A-G

Position:

• chr12-28002147-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 0.0915 in 152,168 control chromosomes in the GnomAD database, including 744 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 0.091 (744 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.181 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: 0.0915 AC: 13911 AN: 152052 Hom.: 741 Cov.: 31

Gnomad AFR AF: 0.0384

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0703

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.0887

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

GnomAD4 genome AF: 0.0915 AC: 13923 AN: 152168 Hom.: 744 Cov.: 31 AF XY: 0.0902 AC XY: 6708 AN XY: 74372

Gnomad4 AFR AF: 0.0387

Gnomad4 AMR AF: 0.0849

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.0703

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.0882

Alfa AF: 0.106 Hom.: 244

Bravo AF: 0.0911

Asia WGS AF: 0.141 AC: 491 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.6
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10771399; hg19: chr12-28155080;