chr12-28853059-T-C

Variant names:

• chr12-28853059-T-C
• rs4931109

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 0.863 in 152,092 control chromosomes in the GnomAD database, including 56,990 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 0.86 (56990 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.894 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131225 AN: 151974 Hom.: 56956 Cov.: 32

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.827

Gnomad ASJ AF: 0.894

Gnomad EAS AF: 0.638

Gnomad SAS AF: 0.771

Gnomad FIN AF: 0.922

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.887

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

GnomAD4 genome AF: 0.863 AC: 131319 AN: 152092 Hom.: 56990 Cov.: 32 AF XY: 0.861 AC XY: 63971 AN XY: 74322

African (AFR) AF: 0.839 AC: 34812 AN: 41512

American (AMR) AF: 0.827 AC: 12624 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.894 AC: 3102 AN: 3470

East Asian (EAS) AF: 0.638 AC: 3271 AN: 5126

South Asian (SAS) AF: 0.771 AC: 3713 AN: 4818

European-Finnish (FIN) AF: 0.922 AC: 9771 AN: 10602

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61187 AN: 67986

Other (OTH) AF: 0.888 AC: 1875 AN: 2112

Alfa AF: 0.877 Hom.: 7134

Bravo AF: 0.856

Asia WGS AF: 0.750 AC: 2611 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	2.9
DANN	Benign	0.73
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs4931109; hg19: chr12-29005992;