chr12-102486344-T-C

Variant names:

• chr12-102486344-T-C
• rs9919733
• XR_007063427.1:n.34902+2456T>C

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+2456T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,190 control chromosomes in the GnomAD database, including 2,166 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 0.13 (2166 hom., cov: 32)
• Consequence: LINC02456 XR_007063427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 3 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.278 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19767 AN: 152072 Hom.: 2151 Cov.: 32

Gnomad AFR AF: 0.280

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.0511

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.0830

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0413

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.130 AC: 19840 AN: 152190 Hom.: 2166 Cov.: 32 AF XY: 0.133 AC XY: 9868 AN XY: 74422

African (AFR) AF: 0.280 AC: 11628 AN: 41504

American (AMR) AF: 0.115 AC: 1757 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0511 AC: 177 AN: 3466

East Asian (EAS) AF: 0.290 AC: 1503 AN: 5188

South Asian (SAS) AF: 0.0833 AC: 402 AN: 4826

European-Finnish (FIN) AF: 0.114 AC: 1209 AN: 10590

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0412 AC: 2805 AN: 68006

Other (OTH) AF: 0.124 AC: 263 AN: 2114

Alfa AF: 0.0648 Hom.: 1026

Bravo AF: 0.140

Asia WGS AF: 0.222 AC: 771 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.64
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs9919733; hg19: chr12-102880122;