11-11116111-C-T

Variant names:

• chr11-11116111-C-T
• rs12794717
• ENST00000647635.1:n.159-1725C>T

Variant summary

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

The ENST00000647635.1(LINC02752):​n.159-1725C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.322 in 151,794 control chromosomes in the GnomAD database, including 8,726 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 0.32 (8726 hom., cov: 31)
• Consequence: LINC02752 ENST00000647635.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 1 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02752	NR_187401.1	n.97+630C>T		intron_variant	Intron 1 of 2
LINC02752	NR_187402.1	n.97+630C>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02752	ENST00000647635.1	n.159-1725C>T		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48850 AN: 151676 Hom.: 8736 Cov.: 31

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.479

Gnomad AMR AF: 0.420

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.298

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.322 AC: 48850 AN: 151794 Hom.: 8726 Cov.: 31 AF XY: 0.319 AC XY: 23647 AN XY: 74180

African (AFR) AF: 0.172 AC: 7112 AN: 41382

American (AMR) AF: 0.420 AC: 6411 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1365 AN: 3466

East Asian (EAS) AF: 0.314 AC: 1614 AN: 5148

South Asian (SAS) AF: 0.257 AC: 1234 AN: 4808

European-Finnish (FIN) AF: 0.298 AC: 3138 AN: 10518

Middle Eastern (MID) AF: 0.366 AC: 107 AN: 292

European-Non Finnish (NFE) AF: 0.393 AC: 26654 AN: 67900

Other (OTH) AF: 0.370 AC: 778 AN: 2104

Alfa AF: 0.360 Hom.: 3521

Bravo AF: 0.329

Asia WGS AF: 0.279 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	3.2
DANN	Benign	0.62
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs12794717; hg19: chr11-11137658;