rs901398

Variant names:

• chr11-11074674-C-T
• rs901398
• ENST00000647635.1:n.159-43162C>T

Variant summary

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

The ENST00000647635.1(LINC02752):​n.159-43162C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.672 in 152,020 control chromosomes in the GnomAD database, including 34,444 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 0.67 (34444 hom., cov: 32)
• Consequence: LINC02752 ENST00000647635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 15 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000647635.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02752	ENST00000647635.1		n.159-43162C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.672 AC: 102091 AN: 151900 Hom.: 34425 Cov.: 32

Gnomad AFR AF: 0.637

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.674

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.671

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.672 AC: 102157 AN: 152020 Hom.: 34444 Cov.: 32 AF XY: 0.674 AC XY: 50079 AN XY: 74290

African (AFR) AF: 0.637 AC: 26415 AN: 41472

American (AMR) AF: 0.673 AC: 10292 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2424 AN: 3464

East Asian (EAS) AF: 0.712 AC: 3675 AN: 5158

South Asian (SAS) AF: 0.695 AC: 3341 AN: 4808

European-Finnish (FIN) AF: 0.671 AC: 7086 AN: 10564

Middle Eastern (MID) AF: 0.748 AC: 220 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46728 AN: 67954

Other (OTH) AF: 0.687 AC: 1453 AN: 2114

Alfa AF: 0.680 Hom.: 66682

Bravo AF: 0.670

Asia WGS AF: 0.691 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs901398; hg19: chr11-11096221; COSMIC: COSV53392023;