chr12-112904793-T-G

Variant names:

• chr12-112904793-T-G
• rs1557865

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 0.873 in 152,244 control chromosomes in the GnomAD database, including 58,463 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 0.87 (58463 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 8 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 (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.872 AC: 132710 AN: 152126 Hom.: 58403 Cov.: 32

Gnomad AFR AF: 0.969

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.910

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.867

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.811

Gnomad OTH AF: 0.858

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

GnomAD4 genome AF: 0.873 AC: 132834 AN: 152244 Hom.: 58463 Cov.: 32 AF XY: 0.875 AC XY: 65112 AN XY: 74426

African (AFR) AF: 0.969 AC: 40272 AN: 41548

American (AMR) AF: 0.910 AC: 13930 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2446 AN: 3466

East Asian (EAS) AF: 0.999 AC: 5183 AN: 5190

South Asian (SAS) AF: 0.800 AC: 3854 AN: 4816

European-Finnish (FIN) AF: 0.867 AC: 9187 AN: 10592

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.811 AC: 55184 AN: 68008

Other (OTH) AF: 0.860 AC: 1819 AN: 2116

Alfa AF: 0.827 Hom.: 3009

Bravo AF: 0.884

Asia WGS AF: 0.896 AC: 3116 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.0
DANN	Benign	0.45
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs1557865; hg19: chr12-113342598;