12-102487918-T-G

Variant names:

• chr12-102487918-T-G
• rs35765
• XR_007063427.1:n.34902+4030T>G

Variant summary

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

The XR_007063427.1(LINC02456):​n.34902+4030T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,106 control chromosomes in the GnomAD database, including 54,524 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 0.84 (54524 hom., cov: 33)
• Consequence: LINC02456 XR_007063427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122
• Publications: 18 publications found

Genes affected

LINC02456 (HGNC:53389): (long intergenic non-protein coding RNA 2456)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.918 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: 0.843 AC: 128197 AN: 151988 Hom.: 54480 Cov.: 33

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.819

Gnomad EAS AF: 0.940

Gnomad SAS AF: 0.858

Gnomad FIN AF: 0.908

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.880

Gnomad OTH AF: 0.856

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

GnomAD4 genome AF: 0.843 AC: 128301 AN: 152106 Hom.: 54524 Cov.: 33 AF XY: 0.846 AC XY: 62930 AN XY: 74344

African (AFR) AF: 0.738 AC: 30607 AN: 41474

American (AMR) AF: 0.887 AC: 13558 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.819 AC: 2841 AN: 3468

East Asian (EAS) AF: 0.940 AC: 4864 AN: 5174

South Asian (SAS) AF: 0.858 AC: 4129 AN: 4814

European-Finnish (FIN) AF: 0.908 AC: 9605 AN: 10576

Middle Eastern (MID) AF: 0.827 AC: 243 AN: 294

European-Non Finnish (NFE) AF: 0.880 AC: 59835 AN: 68004

Other (OTH) AF: 0.858 AC: 1806 AN: 2106

Alfa AF: 0.864 Hom.: 34351

Bravo AF: 0.838

Asia WGS AF: 0.918 AC: 3190 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.1
DANN	Benign	0.48
PhyloP100		-0.12

Splicing

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

Other links and lift over

dbSNP: rs35765; hg19: chr12-102881696;