ENST00000451284.6:n.494-723C>T

Variant names:

• chr3-25864102-G-A
• rs4481118
• ENST00000451284.6:n.494-723C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000451284.6(LINC00692):​n.494-723C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.655 in 151,998 control chromosomes in the GnomAD database, including 37,975 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 0.65 (37975 hom., cov: 31)
• Consequence: LINC00692 ENST00000451284.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170
• Publications: 1 publications found

Genes affected

LINC00692 (HGNC:27708): (long intergenic non-protein coding RNA 692)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000451284.6. 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
	LINC00692	NR_034055.1		n.441-723C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00692	ENST00000451284.6	TSL:1	n.494-723C>T		intron	N/A
	LINC00692	ENST00000496997.1	TSL:5	n.410-5304C>T		intron	N/A
	LINC00692	ENST00000655652.1		n.451-723C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.655 AC: 99457 AN: 151880 Hom.: 37962 Cov.: 31

Gnomad AFR AF: 0.230

Gnomad AMI AF: 0.770

Gnomad AMR AF: 0.795

Gnomad ASJ AF: 0.843

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.814

Gnomad MID AF: 0.843

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.702

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

GnomAD4 genome AF: 0.655 AC: 99489 AN: 151998 Hom.: 37975 Cov.: 31 AF XY: 0.661 AC XY: 49140 AN XY: 74294

African (AFR) AF: 0.230 AC: 9527 AN: 41420

American (AMR) AF: 0.795 AC: 12145 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.843 AC: 2926 AN: 3470

East Asian (EAS) AF: 0.960 AC: 4969 AN: 5174

South Asian (SAS) AF: 0.741 AC: 3578 AN: 4828

European-Finnish (FIN) AF: 0.814 AC: 8622 AN: 10590

Middle Eastern (MID) AF: 0.841 AC: 244 AN: 290

European-Non Finnish (NFE) AF: 0.814 AC: 55291 AN: 67940

Other (OTH) AF: 0.706 AC: 1488 AN: 2108

Alfa AF: 0.618 Hom.: 3010

Bravo AF: 0.636

Asia WGS AF: 0.754 AC: 2610 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	4.4
DANN	Benign	0.72
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4481118; hg19: chr3-25905593;