12-102497908-T-C

Variant names:

• chr12-102497908-T-C
• rs7965399
• XR_007063427.1:n.34902+14020T>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+14020T>C 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 152,196 control chromosomes in the GnomAD database, including 2,399 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 (2399 hom., cov: 32)
• Consequence: LINC02456 XR_007063427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 26 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+14020T>C		intron_variant	Intron 11 of 12

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20657 AN: 152078 Hom.: 2380 Cov.: 32

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.100

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0415

Gnomad OTH AF: 0.120

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

GnomAD4 genome AF: 0.136 AC: 20731 AN: 152196 Hom.: 2399 Cov.: 32 AF XY: 0.138 AC XY: 10262 AN XY: 74396

African (AFR) AF: 0.301 AC: 12493 AN: 41502

American (AMR) AF: 0.116 AC: 1771 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0510 AC: 177 AN: 3470

East Asian (EAS) AF: 0.286 AC: 1484 AN: 5186

South Asian (SAS) AF: 0.0844 AC: 407 AN: 4824

European-Finnish (FIN) AF: 0.115 AC: 1217 AN: 10598

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

European-Non Finnish (NFE) AF: 0.0415 AC: 2821 AN: 68014

Other (OTH) AF: 0.126 AC: 265 AN: 2110

Alfa AF: 0.0719 Hom.: 3062

Bravo AF: 0.147

Asia WGS AF: 0.222 AC: 768 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.10
DANN	Benign	0.42
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7965399; hg19: chr12-102891686;