rs2514930

chr11-91200629-A-T

Variant summary

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

The NR_183632.1(LINC02748):n.778+7141A>T variant causes a intron, non coding transcript 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 NR_183632.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.491

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02748	NR_183632.1	n.778+7141A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02748	ENST00000526509.2	n.745+7141A>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.322

Gnomad4 AMR AF: 0.227

Gnomad4 ASJ AF: 0.193

Gnomad4 EAS AF: 0.345

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.206

Gnomad4 NFE AF: 0.224

Gnomad4 OTH AF: 0.248

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.32
Dann	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2514930; hg19: chr11-90933797;