ENST00000649115.1:n.1008+274A>G

Variant names:

• chr11-128175071-A-G
• rs7948482
• ENST00000649115.1:n.1008+274A>G

Variant summary

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

The ENST00000649115.1(LINC02725):​n.1008+274A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,108 control chromosomes in the GnomAD database, including 4,895 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 0.24 (4895 hom., cov: 33)
• Consequence: LINC02725 ENST00000649115.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649115.1. 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.703-5389A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02725	ENST00000649115.1		n.1008+274A>G		intron	N/A
	LINC02725	ENST00000654938.1		n.1102+274A>G		intron	N/A
	LINC02725	ENST00000664091.1		n.485-5389A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36537 AN: 151990 Hom.: 4886 Cov.: 33

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.298

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.170

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.270

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

GnomAD4 genome AF: 0.240 AC: 36574 AN: 152108 Hom.: 4895 Cov.: 33 AF XY: 0.240 AC XY: 17870 AN XY: 74372

African (AFR) AF: 0.356 AC: 14745 AN: 41464

American (AMR) AF: 0.280 AC: 4281 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.251 AC: 869 AN: 3466

East Asian (EAS) AF: 0.297 AC: 1533 AN: 5166

South Asian (SAS) AF: 0.217 AC: 1046 AN: 4824

European-Finnish (FIN) AF: 0.170 AC: 1797 AN: 10586

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11524 AN: 68000

Other (OTH) AF: 0.273 AC: 576 AN: 2112

Alfa AF: 0.191 Hom.: 13240

Bravo AF: 0.255

Asia WGS AF: 0.266 AC: 926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.1
DANN	Benign	0.81
PhyloP100		-0.094

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7948482;

hg19: chr11-128044966;