rs35766

Variant names:

• chr12-102486695-C-T
• rs35766
• XR_007063427.1:n.34902+2807C>T

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+2807C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.711 in 151,990 control chromosomes in the GnomAD database, including 40,483 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 0.71 (40483 hom., cov: 31)
• Consequence: LINC02456 XR_007063427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.227
• Publications: 14 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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.832 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+2807C>T		intron_variant	Intron 11 of 12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108033 AN: 151872 Hom.: 40487 Cov.: 31

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.771

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.775

Gnomad FIN AF: 0.794

Gnomad MID AF: 0.804

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.711 AC: 108061 AN: 151990 Hom.: 40483 Cov.: 31 AF XY: 0.712 AC XY: 52877 AN XY: 74300

African (AFR) AF: 0.452 AC: 18693 AN: 41392

American (AMR) AF: 0.771 AC: 11781 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2643 AN: 3472

East Asian (EAS) AF: 0.650 AC: 3354 AN: 5158

South Asian (SAS) AF: 0.774 AC: 3728 AN: 4816

European-Finnish (FIN) AF: 0.794 AC: 8397 AN: 10578

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.838 AC: 56965 AN: 67986

Other (OTH) AF: 0.730 AC: 1540 AN: 2110

Alfa AF: 0.806 Hom.: 32877

Bravo AF: 0.695

Asia WGS AF: 0.695 AC: 2415 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	4.0
DANN	Benign	0.67
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs35766; hg19: chr12-102880473;