rs4481118

chr3-25864102-G-Achr3-25864102-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_034055.1(LINC00692):n.441-723C>T variant causes a intron, non coding transcript 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 NR_034055.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.170

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00692	NR_034055.1	n.441-723C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00692	ENST00000451284.6	n.494-723C>T		intron_variant, non_coding_transcript_variant		1
LINC00692	ENST00000655652.1	n.451-723C>T		intron_variant, non_coding_transcript_variant
LINC00692	ENST00000496997.1	n.410-5304C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.230

Gnomad4 AMR AF: 0.795

Gnomad4 ASJ AF: 0.843

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.741

Gnomad4 FIN AF: 0.814

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.706

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	4.4
Dann	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4481118; hg19: chr3-25905593;