chr12-102501478-A-G

Variant names:

• chr12-102501478-A-G
• rs11111285
• XR_007063427.1:n.34902+17590A>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+17590A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,164 control chromosomes in the GnomAD database, including 2,411 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 0.14 (2411 hom., cov: 32)
• Consequence: LINC02456 XR_007063427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.953
• Publications: 6 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 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: 0.136 AC: 20688 AN: 152046 Hom.: 2391 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.287

Gnomad SAS AF: 0.0831

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.136 AC: 20768 AN: 152164 Hom.: 2411 Cov.: 32 AF XY: 0.138 AC XY: 10300 AN XY: 74426

African (AFR) AF: 0.302 AC: 12517 AN: 41460

American (AMR) AF: 0.116 AC: 1774 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3468

East Asian (EAS) AF: 0.288 AC: 1487 AN: 5172

South Asian (SAS) AF: 0.0833 AC: 402 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1220 AN: 10606

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

European-Non Finnish (NFE) AF: 0.0415 AC: 2825 AN: 68020

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.101 Hom.: 269

Bravo AF: 0.147

Asia WGS AF: 0.224 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.28
DANN	Benign	0.25
PhyloP100		-0.95

Splicing

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

Other links and lift over

dbSNP: rs11111285; hg19: chr12-102895256;