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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+4030T>G		intron_variant	Intron 11 of 12

Ensembl

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

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 v4.3

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;