rs2912600

Variant names:

• chr15-26475396-A-G
• rs2912600
• ENST00000660088.2:n.425+2325T>C

Variant summary

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

The ENST00000660088.2(ENSG00000287280):​n.425+2325T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 152,126 control chromosomes in the GnomAD database, including 9,402 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 0.28 (9402 hom., cov: 32)
• Consequence: ENSG00000287280 ENST00000660088.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02248	XR_001751453.2	n.2695-14116A>G		intron_variant	Intron 5 of 5
LOC105370740	XR_007064791.1	n.418+2325T>C		intron_variant	Intron 1 of 8
LOC105370740	XR_007064792.1	n.418+2325T>C		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287280	ENST00000660088.2	n.425+2325T>C		intron_variant	Intron 2 of 6
ENSG00000287280	ENST00000826682.1	n.390+2325T>C		intron_variant	Intron 2 of 4
ENSG00000287280	ENST00000826683.1	n.425+2325T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 42017 AN: 152008 Hom.: 9374 Cov.: 32

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.255

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.162

Gnomad FIN AF: 0.146

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.277 AC: 42086 AN: 152126 Hom.: 9402 Cov.: 32 AF XY: 0.273 AC XY: 20271 AN XY: 74384

African (AFR) AF: 0.622 AC: 25797 AN: 41460

American (AMR) AF: 0.215 AC: 3286 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.255 AC: 885 AN: 3470

East Asian (EAS) AF: 0.155 AC: 799 AN: 5154

South Asian (SAS) AF: 0.161 AC: 776 AN: 4822

European-Finnish (FIN) AF: 0.146 AC: 1551 AN: 10606

Middle Eastern (MID) AF: 0.255 AC: 75 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8327 AN: 68008

Other (OTH) AF: 0.274 AC: 579 AN: 2112

Alfa AF: 0.178 Hom.: 7213

Bravo AF: 0.300

Asia WGS AF: 0.204 AC: 713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.33
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2912600; hg19: chr15-26720543;