ENST00000715768.1:n.374+10354T>G

Variant names:

• chr8-61954551-T-G
• rs344286
• ENST00000715768.1:n.374+10354T>G

Variant summary

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

The ENST00000715768.1(LINC02842):​n.374+10354T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.722 in 151,546 control chromosomes in the GnomAD database, including 40,635 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 0.72 (40635 hom., cov: 29)
• Consequence: LINC02842 ENST00000715768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 6 publications found

Genes affected

LINC02842 (HGNC:54378): (long intergenic non-protein coding RNA 2842)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02842	ENST00000715768.1	n.374+10354T>G		intron_variant	Intron 4 of 10
LINC02842	ENST00000829200.1	n.511-17673T>G		intron_variant	Intron 3 of 4
LINC02842	ENST00000850662.1	n.345-32764T>G		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.722 AC: 109262 AN: 151428 Hom.: 40591 Cov.: 29

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.747

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.704

Gnomad FIN AF: 0.606

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.664

Gnomad OTH AF: 0.706

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

GnomAD4 genome AF: 0.722 AC: 109358 AN: 151546 Hom.: 40635 Cov.: 29 AF XY: 0.716 AC XY: 52947 AN XY: 73996

African (AFR) AF: 0.906 AC: 37498 AN: 41380

American (AMR) AF: 0.595 AC: 9029 AN: 15178

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1914 AN: 3456

East Asian (EAS) AF: 0.749 AC: 3826 AN: 5106

South Asian (SAS) AF: 0.703 AC: 3371 AN: 4794

European-Finnish (FIN) AF: 0.606 AC: 6350 AN: 10486

Middle Eastern (MID) AF: 0.610 AC: 178 AN: 292

European-Non Finnish (NFE) AF: 0.664 AC: 45009 AN: 67828

Other (OTH) AF: 0.711 AC: 1502 AN: 2114

Alfa AF: 0.672 Hom.: 12442

Bravo AF: 0.731

Asia WGS AF: 0.739 AC: 2574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.54
DANN	Benign	0.61
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs344286; hg19: chr8-62867110;