8-61954382-A-T

Variant names:

• chr8-61954382-A-T
• rs344287
• ENST00000715768.1:n.374+10185A>T

Variant summary

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

The ENST00000715768.1(LINC02842):​n.374+10185A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.721 in 151,820 control chromosomes in the GnomAD database, including 40,709 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 (40709 hom., cov: 31)
• Consequence: LINC02842 ENST00000715768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.310
• Publications: 2 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715768.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02842	ENST00000715768.1		n.374+10185A>T		intron	N/A
	LINC02842	ENST00000829200.1		n.511-17842A>T		intron	N/A
	LINC02842	ENST00000850662.1		n.345-32933A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.721 AC: 109435 AN: 151702 Hom.: 40665 Cov.: 31

Gnomad AFR AF: 0.906

Gnomad AMI AF: 0.751

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.554

Gnomad EAS AF: 0.748

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.721 AC: 109531 AN: 151820 Hom.: 40709 Cov.: 31 AF XY: 0.715 AC XY: 53011 AN XY: 74124

African (AFR) AF: 0.906 AC: 37577 AN: 41462

American (AMR) AF: 0.595 AC: 9040 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.554 AC: 1917 AN: 3462

East Asian (EAS) AF: 0.748 AC: 3844 AN: 5142

South Asian (SAS) AF: 0.703 AC: 3372 AN: 4800

European-Finnish (FIN) AF: 0.605 AC: 6355 AN: 10512

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.663 AC: 45067 AN: 67930

Other (OTH) AF: 0.712 AC: 1501 AN: 2108

Alfa AF: 0.685 Hom.: 4523

Bravo AF: 0.731

Asia WGS AF: 0.739 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	4.9
DANN	Benign	0.60
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs344287; hg19: chr8-62866941;