rs1394119

chr11-11130773-T-G

Variant summary

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

The ENST00000525758.1(LINC02752):n.108+10238T>G 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 0.384 in 151,980 control chromosomes in the GnomAD database, including 12,305 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 0.38 (12305 hom., cov: 32)
• Consequence: LINC02752 ENST00000525758.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.39

Genes affected

LINC02752 (HGNC:54272): (long intergenic non-protein coding RNA 2752)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02752	XR_007062591.1	n.98+11934T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02752	ENST00000525758.1	n.108+10238T>G		intron_variant, non_coding_transcript_variant		1
LINC02752	ENST00000647635.1	n.272+12824T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58357 AN: 151860 Hom.: 12306 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.485

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.404

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.384 AC: 58373 AN: 151980 Hom.: 12305 Cov.: 32 AF XY: 0.383 AC XY: 28424 AN XY: 74278

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.467

Gnomad4 ASJ AF: 0.485

Gnomad4 EAS AF: 0.245

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.404

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.409

Alfa AF: 0.412 Hom.: 2031

Bravo AF: 0.381

Asia WGS AF: 0.277 AC: 961 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.56
Dann	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1394119; hg19: chr11-11152320;