chr15-26447113-C-G

Variant names:

• chr15-26447113-C-G
• rs6576575
• ENST00000451579.3:n.945C>G

Variant summary

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

The ENST00000451579.3(LINC02248):​n.945C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,110 control chromosomes in the GnomAD database, including 3,849 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 0.17 (3849 hom., cov: 32)
• Consequence: LINC02248 ENST00000451579.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.290
• Publications: 3 publications found

Genes affected

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

ENSG00000287280 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.392 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02248	XR_001751449.2	n.873C>G		non_coding_transcript_exon_variant	Exon 2 of 5
LINC02248	XR_001751451.2	n.873C>G		non_coding_transcript_exon_variant	Exon 2 of 6
LINC02248	XR_001751452.2	n.873C>G		non_coding_transcript_exon_variant	Exon 2 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02248	ENST00000451579.3	n.945C>G		non_coding_transcript_exon_variant	Exon 3 of 4	3
LINC02248	ENST00000658140.1	n.893C>G		non_coding_transcript_exon_variant	Exon 2 of 5
LINC02248	ENST00000662421.2	n.858C>G		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26251 AN: 151992 Hom.: 3827 Cov.: 32

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.108

Gnomad FIN AF: 0.0264

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.0681

Gnomad OTH AF: 0.186

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

GnomAD4 genome AF: 0.173 AC: 26328 AN: 152110 Hom.: 3849 Cov.: 32 AF XY: 0.171 AC XY: 12698 AN XY: 74356

African (AFR) AF: 0.397 AC: 16466 AN: 41434

American (AMR) AF: 0.173 AC: 2651 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 610 AN: 3472

East Asian (EAS) AF: 0.124 AC: 640 AN: 5176

South Asian (SAS) AF: 0.109 AC: 526 AN: 4826

European-Finnish (FIN) AF: 0.0264 AC: 280 AN: 10606

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.0680 AC: 4627 AN: 67996

Other (OTH) AF: 0.185 AC: 391 AN: 2110

Alfa AF: 0.0435 Hom.: 76

Bravo AF: 0.194

Asia WGS AF: 0.116 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.43
DANN	Benign	0.43
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs6576575; hg19: chr15-26692260;