rs901398

Positions:

• chr11-11074674-C-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000647635.1	n.159-43162C>T		intron_variant, non_coding_transcript_variant

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;