ENST00000488348.1:n.188+218G>T

Variant names:

• chr3-84885341-G-T
• rs649851
• ENST00000488348.1:n.188+218G>T

Variant summary

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

The ENST00000488348.1(LINC02025):​n.188+218G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,942 control chromosomes in the GnomAD database, including 14,441 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 0.43 (14441 hom., cov: 32)
• Consequence: LINC02025 ENST00000488348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 2 publications found

Genes affected

LINC02025 (HGNC:52860): (long intergenic non-protein coding RNA 2025)

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 (AFR) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000488348.1. 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
	LINC02025	NR_147147.1		n.195+218G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02025	ENST00000488348.1	TSL:3	n.188+218G>T		intron	N/A
	LINC02025	ENST00000661831.1		n.223+296G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64868 AN: 151822 Hom.: 14428 Cov.: 32

Gnomad AFR AF: 0.571

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.409

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.374

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.427 AC: 64934 AN: 151942 Hom.: 14441 Cov.: 32 AF XY: 0.433 AC XY: 32165 AN XY: 74284

African (AFR) AF: 0.571 AC: 23622 AN: 41404

American (AMR) AF: 0.409 AC: 6251 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1211 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2256 AN: 5126

South Asian (SAS) AF: 0.372 AC: 1791 AN: 4820

European-Finnish (FIN) AF: 0.487 AC: 5144 AN: 10566

Middle Eastern (MID) AF: 0.439 AC: 129 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23463 AN: 67976

Other (OTH) AF: 0.378 AC: 793 AN: 2098

Alfa AF: 0.403 Hom.: 1650

Bravo AF: 0.427

Asia WGS AF: 0.449 AC: 1566 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	1.2
DANN	Benign	0.23
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs649851; hg19: chr3-84934492;