12-28084798-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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105369710	XR_931462.3	n.4213C>A		non_coding_transcript_exon_variant	Exon 3 of 3
LOC105369710	XR_931461.3	n.156-20911C>A		intron_variant	Intron 2 of 2

Ensembl

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

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 v4.3

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;