chr12-102486695-C-T

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.

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: 0.711 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 v4.9

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;