ENST00000525097.1:n.243+29112A>G

Variant names:

• chr11-29366251-T-C
• rs2793471
• ENST00000525097.1:n.243+29112A>G

Variant summary

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

The ENST00000525097.1(LINC02755):​n.243+29112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 151,740 control chromosomes in the GnomAD database, including 10,439 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 0.35 (10439 hom., cov: 31)
• Consequence: LINC02755 ENST00000525097.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.354
• Publications: 2 publications found

Genes affected

LINC02755 (HGNC:54275): (long intergenic non-protein coding RNA 2755)

ENSG00000254526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000525097.1. 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
	LINC02755	NR_183753.1		n.423+12079A>G		intron	N/A
	LINC02755	NR_183754.1		n.298+29112A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02755	ENST00000525097.1	TSL:3	n.243+29112A>G		intron	N/A
	LINC02755	ENST00000528553.2	TSL:3	n.408+12079A>G		intron	N/A
	LINC02755	ENST00000653616.1		n.423+12079A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53313 AN: 151622 Hom.: 10438 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.441

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.495

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.356

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

GnomAD4 genome AF: 0.351 AC: 53320 AN: 151740 Hom.: 10439 Cov.: 31 AF XY: 0.353 AC XY: 26192 AN XY: 74154

African (AFR) AF: 0.193 AC: 8008 AN: 41442

American (AMR) AF: 0.248 AC: 3777 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1913 AN: 3466

East Asian (EAS) AF: 0.425 AC: 2150 AN: 5058

South Asian (SAS) AF: 0.427 AC: 2057 AN: 4814

European-Finnish (FIN) AF: 0.495 AC: 5233 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.426 AC: 28921 AN: 67844

Other (OTH) AF: 0.357 AC: 751 AN: 2106

Alfa AF: 0.407 Hom.: 8231

Bravo AF: 0.326

Asia WGS AF: 0.392 AC: 1362 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.3
DANN	Benign	0.50
PhyloP100		0.35

Splicing

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

Other links and lift over

dbSNP: rs2793471; hg19: chr11-29387798;