rs901398

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000647635.1	n.159-43162C>T		intron_variant	Intron 1 of 6

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

Gnomad4 AFR AF: 0.637

Gnomad4 AMR AF: 0.673

Gnomad4 ASJ AF: 0.700

Gnomad4 EAS AF: 0.712

Gnomad4 SAS AF: 0.695

Gnomad4 FIN AF: 0.671

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.687

Alfa AF: 0.682 Hom.: 18057

Bravo AF: 0.670

Asia WGS AF: 0.691 AC: 2406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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