ENST00000715768.1:n.374+15013A>T

Variant names:

• chr8-61959210-A-T
• rs684872
• ENST00000715768.1:n.374+15013A>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+15013A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,730 control chromosomes in the GnomAD database, including 16,623 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 0.46 (16623 hom., cov: 30)
• Consequence: LINC02842 ENST00000715768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.36
• Publications: 4 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=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.539 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+15013A>T		intron_variant	Intron 4 of 10
LINC02842	ENST00000829200.1	n.511-13014A>T		intron_variant	Intron 3 of 4
LINC02842	ENST00000850662.1	n.345-28105A>T		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.464 AC: 70366 AN: 151612 Hom.: 16619 Cov.: 30

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.464 AC: 70394 AN: 151730 Hom.: 16623 Cov.: 30 AF XY: 0.463 AC XY: 34326 AN XY: 74126

African (AFR) AF: 0.398 AC: 16474 AN: 41400

American (AMR) AF: 0.411 AC: 6265 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3466

East Asian (EAS) AF: 0.472 AC: 2407 AN: 5104

South Asian (SAS) AF: 0.557 AC: 2674 AN: 4802

European-Finnish (FIN) AF: 0.485 AC: 5114 AN: 10542

Middle Eastern (MID) AF: 0.370 AC: 108 AN: 292

European-Non Finnish (NFE) AF: 0.511 AC: 34670 AN: 67874

Other (OTH) AF: 0.467 AC: 987 AN: 2114

Alfa AF: 0.479 Hom.: 2211

Bravo AF: 0.456

Asia WGS AF: 0.531 AC: 1847 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
DANN	Benign	0.93
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs684872; hg19: chr8-62871769;