rs952361

Positions:

• chr11-11164418-G-A
• chr11-11164418-G-C
• chr11-11164418-G-T

Variant summary

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

The ENST00000525758.1(LINC02752):​n.109-3405G>A 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 0.48 in 151,556 control chromosomes in the GnomAD database, including 17,882 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 0.48 (17882 hom., cov: 30)
• Consequence: LINC02752 ENST00000525758.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338

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 (AFR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02752	XR_007062591.1	n.99-3405G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02752	ENST00000525758.1	n.109-3405G>A		intron_variant, non_coding_transcript_variant		1
LINC02752	ENST00000647635.1	n.273-4663G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72593 AN: 151440 Hom.: 17840 Cov.: 30

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.418

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.480 AC: 72699 AN: 151556 Hom.: 17882 Cov.: 30 AF XY: 0.478 AC XY: 35365 AN XY: 74016

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.418

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.432

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.441

Gnomad4 OTH AF: 0.456

Alfa AF: 0.438 Hom.: 7197

Bravo AF: 0.485

Asia WGS AF: 0.468 AC: 1626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs952361; hg19: chr11-11185965;