12-102497974-A-G

Variant names:

• chr12-102497974-A-G
• rs7978742
• XR_007063427.1:n.34902+14086A>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+14086A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,152 control chromosomes in the GnomAD database, including 2,426 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 (2426 hom., cov: 32)
• Consequence: LINC02456 XR_007063427.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.897
• Publications: 4 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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.298 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02456	XR_007063427.1	n.34902+14086A>G		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: 20730 AN: 152036 Hom.: 2407 Cov.: 32

Gnomad AFR AF: 0.302

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.0510

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.0838

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: 0.137 AC: 20808 AN: 152152 Hom.: 2426 Cov.: 32 AF XY: 0.139 AC XY: 10303 AN XY: 74376

African (AFR) AF: 0.303 AC: 12561 AN: 41472

American (AMR) AF: 0.116 AC: 1775 AN: 15272

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

East Asian (EAS) AF: 0.286 AC: 1482 AN: 5182

South Asian (SAS) AF: 0.0841 AC: 405 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1218 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0415 AC: 2823 AN: 68008

Other (OTH) AF: 0.127 AC: 268 AN: 2116

Alfa AF: 0.0647 Hom.: 363

Bravo AF: 0.147

Asia WGS AF: 0.223 AC: 773 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.95
DANN	Benign	0.38
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs7978742; hg19: chr12-102891752;