rs2912602

Variant names:

• chr15-26474092-G-A
• rs2912602
• ENST00000660088.2:n.426-2995C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000660088.2(ENSG00000287280):​n.426-2995C>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 ENST00000660088.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.693
• Publications: 4 publications found

Genes affected

ENSG00000287280 (HGNC:):

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC02248	XR_001751453.2	n.2695-15420G>A		intron_variant	Intron 5 of 5
LOC105370740	XR_007064791.1	n.419-2995C>T		intron_variant	Intron 1 of 8
LOC105370740	XR_007064792.1	n.419-2995C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287280	ENST00000660088.2	n.426-2995C>T		intron_variant	Intron 2 of 6
ENSG00000287280	ENST00000826682.1	n.391-2995C>T		intron_variant	Intron 2 of 4
ENSG00000287280	ENST00000826683.1	n.426-3197C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.375 AC: 15556 AN: 41452

American (AMR) AF: 0.0916 AC: 1401 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.212 AC: 735 AN: 3472

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5174

South Asian (SAS) AF: 0.0513 AC: 247 AN: 4818

European-Finnish (FIN) AF: 0.0671 AC: 711 AN: 10602

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0674 AC: 4583 AN: 68010

Other (OTH) AF: 0.144 AC: 303 AN: 2110

Alfa AF: 0.0975 Hom.: 2411

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
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs2912602; hg19: chr15-26719239;