chr12-28059434-A-G

Variant names:

• chr12-28059434-A-G
• rs10492362

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0766 in 152,268 control chromosomes in the GnomAD database, including 554 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 0.077 (554 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.389
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.117 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0765 AC: 11645 AN: 152150 Hom.: 552 Cov.: 32

Gnomad AFR AF: 0.119

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.0765

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.0912

Gnomad FIN AF: 0.117

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0503

Gnomad OTH AF: 0.0578

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

GnomAD4 genome AF: 0.0766 AC: 11667 AN: 152268 Hom.: 554 Cov.: 32 AF XY: 0.0803 AC XY: 5977 AN XY: 74464

African (AFR) AF: 0.119 AC: 4961 AN: 41542

American (AMR) AF: 0.0764 AC: 1169 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0351 AC: 122 AN: 3472

East Asian (EAS) AF: 0.0193 AC: 100 AN: 5182

South Asian (SAS) AF: 0.0912 AC: 440 AN: 4822

European-Finnish (FIN) AF: 0.117 AC: 1239 AN: 10618

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0503 AC: 3422 AN: 68020

Other (OTH) AF: 0.0568 AC: 120 AN: 2114

Alfa AF: 0.0582 Hom.: 71

Bravo AF: 0.0733

Asia WGS AF: 0.0560 AC: 194 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.68
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs10492362; hg19: chr12-28212367;