rs2514930

Variant names:

• chr11-91200629-A-T
• rs2514930
• ENST00000526509.2:n.745+7141A>T

Variant summary

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

The ENST00000526509.2(LINC02748):​n.745+7141A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 151,854 control chromosomes in the GnomAD database, including 5,039 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 0.25 (5039 hom., cov: 32)
• Consequence: LINC02748 ENST00000526509.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491
• Publications: 3 publications found

Genes affected

LINC02748 (HGNC:54267): (long intergenic non-protein coding RNA 2748)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000526509.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02748	NR_183632.1		n.778+7141A>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02748	ENST00000526509.2	TSL:3	n.745+7141A>T		intron	N/A
	LINC02748	ENST00000724586.1		n.755+7141A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38370 AN: 151736 Hom.: 5035 Cov.: 32

Gnomad AFR AF: 0.322

Gnomad AMI AF: 0.232

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.193

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.261

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.253 AC: 38407 AN: 151854 Hom.: 5039 Cov.: 32 AF XY: 0.251 AC XY: 18620 AN XY: 74202

African (AFR) AF: 0.322 AC: 13327 AN: 41436

American (AMR) AF: 0.227 AC: 3460 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.193 AC: 668 AN: 3466

East Asian (EAS) AF: 0.345 AC: 1756 AN: 5094

South Asian (SAS) AF: 0.210 AC: 1010 AN: 4806

European-Finnish (FIN) AF: 0.206 AC: 2187 AN: 10610

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.224 AC: 15186 AN: 67906

Other (OTH) AF: 0.248 AC: 523 AN: 2108

Alfa AF: 0.237 Hom.: 556

Bravo AF: 0.258

Asia WGS AF: 0.267 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.32
DANN	Benign	0.35
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs2514930; hg19: chr11-90933797;