11-128150473-T-C

Variant names:

• chr11-128150473-T-C
• rs1477577
• ENST00000649115.1:n.202-16699T>C

Variant summary

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

The NR_183639.1(LINC02725):​n.485-16699T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.393 in 151,954 control chromosomes in the GnomAD database, including 12,002 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 0.39 (12002 hom., cov: 31)
• Consequence: LINC02725 NR_183639.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.405
• Publications: 7 publications found

Genes affected

LINC02725 (HGNC:54242): (long intergenic non-protein coding RNA 2725)

ENSG00000301990 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183639.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02725	NR_183639.1		n.485-16699T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02725	ENST00000649115.1		n.202-16699T>C		intron	N/A
	LINC02725	ENST00000654938.1		n.485-16699T>C		intron	N/A
	LINC02725	ENST00000664091.1		n.485-29987T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59568 AN: 151836 Hom.: 11971 Cov.: 31

Gnomad AFR AF: 0.422

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.557

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.350

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.393 AC: 59650 AN: 151954 Hom.: 12002 Cov.: 31 AF XY: 0.393 AC XY: 29211 AN XY: 74282

African (AFR) AF: 0.422 AC: 17497 AN: 41428

American (AMR) AF: 0.465 AC: 7101 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1475 AN: 3464

East Asian (EAS) AF: 0.559 AC: 2891 AN: 5176

South Asian (SAS) AF: 0.507 AC: 2438 AN: 4812

European-Finnish (FIN) AF: 0.306 AC: 3231 AN: 10550

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.350 AC: 23760 AN: 67934

Other (OTH) AF: 0.425 AC: 896 AN: 2108

Alfa AF: 0.372 Hom.: 18597

Bravo AF: 0.405

Asia WGS AF: 0.492 AC: 1709 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.44
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs1477577; hg19: chr11-128020368;