rs2912602

Positions:

• chr15-26474092-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660088.1(ENSG00000287280):​n.121-2995C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,136 control chromosomes in the GnomAD database, including 3,345 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 0.16 (3345 hom., cov: 32)
• Consequence: ENSG00000287280 ENST00000660088.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693

Genes affected

ENSG00000287280 (HGNC:):

LINC02248 (HGNC:53147): (long intergenic non-protein coding RNA 2248)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.37 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02248	XR_001751453.2	n.2695-15420G>A		intron_variant
LOC105370740	XR_007064791.1	n.419-2995C>T		intron_variant
LOC105370740	XR_007064792.1	n.419-2995C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287280	ENST00000660088.1	n.121-2995C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23652 AN: 152018 Hom.: 3338 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.212

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.0516

Gnomad FIN AF: 0.0671

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0674

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.156 AC: 23683 AN: 152136 Hom.: 3345 Cov.: 32 AF XY: 0.151 AC XY: 11221 AN XY: 74378

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.212

Gnomad4 EAS AF: 0.00155

Gnomad4 SAS AF: 0.0513

Gnomad4 FIN AF: 0.0671

Gnomad4 NFE AF: 0.0674

Gnomad4 OTH AF: 0.144

Alfa AF: 0.0904 Hom.: 1242

Bravo AF: 0.168

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.7
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2912602; hg19: chr15-26719239;