12-112899358-A-G

Variant names:

• chr12-112899358-A-G
• rs10492028

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 0.734 in 151,776 control chromosomes in the GnomAD database, including 41,940 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 0.73 (41940 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.973 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111272 AN: 151658 Hom.: 41931 Cov.: 29

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.773

Gnomad AMR AF: 0.849

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.996

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.734 AC: 111331 AN: 151776 Hom.: 41940 Cov.: 29 AF XY: 0.739 AC XY: 54765 AN XY: 74154

African (AFR) AF: 0.554 AC: 22905 AN: 41314

American (AMR) AF: 0.848 AC: 12956 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2222 AN: 3464

East Asian (EAS) AF: 0.996 AC: 5154 AN: 5174

South Asian (SAS) AF: 0.780 AC: 3726 AN: 4778

European-Finnish (FIN) AF: 0.797 AC: 8405 AN: 10540

Middle Eastern (MID) AF: 0.690 AC: 203 AN: 294

European-Non Finnish (NFE) AF: 0.787 AC: 53470 AN: 67922

Other (OTH) AF: 0.752 AC: 1588 AN: 2112

Alfa AF: 0.768 Hom.: 60642

Bravo AF: 0.732

Asia WGS AF: 0.822 AC: 2857 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.14
DANN	Benign	0.21
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10492028; hg19: chr12-113337163;