chr12-28084798-G-T

Variant names:

• chr12-28084798-G-T
• rs10843090
• XR_931462.3:n.4213C>A

Variant summary

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

The XR_931462.3(LOC105369710):​n.4213C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.38 in 151,814 control chromosomes in the GnomAD database, including 12,361 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 0.38 (12361 hom., cov: 32)
• Consequence: LOC105369710 XR_931462.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71
• Publications: 2 publications found

Genes affected

LOC105369710 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.479 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: 0.380 AC: 57681 AN: 151696 Hom.: 12353 Cov.: 32

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.380 AC: 57719 AN: 151814 Hom.: 12361 Cov.: 32 AF XY: 0.386 AC XY: 28604 AN XY: 74172

African (AFR) AF: 0.184 AC: 7612 AN: 41440

American (AMR) AF: 0.373 AC: 5689 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1480 AN: 3468

East Asian (EAS) AF: 0.495 AC: 2545 AN: 5138

South Asian (SAS) AF: 0.418 AC: 2009 AN: 4804

European-Finnish (FIN) AF: 0.529 AC: 5573 AN: 10528

Middle Eastern (MID) AF: 0.384 AC: 112 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31612 AN: 67898

Other (OTH) AF: 0.404 AC: 851 AN: 2106

Alfa AF: 0.420 Hom.: 15111

Bravo AF: 0.359

Asia WGS AF: 0.386 AC: 1344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.034
DANN	Benign	0.65
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs10843090; hg19: chr12-28237731;