8-61973294-G-A

Variant names:

• chr8-61973294-G-A
• rs1431918
• ENST00000715768.1:n.375-6931G>A

Variant summary

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

The ENST00000715768.1(LINC02842):​n.375-6931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 151,890 control chromosomes in the GnomAD database, including 9,224 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 0.33 (9224 hom., cov: 32)
• Consequence: LINC02842 ENST00000715768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.91
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.486 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.375-6931G>A		intron_variant	Intron 4 of 10
LINC02842	ENST00000850662.1	n.345-14021G>A		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49467 AN: 151772 Hom.: 9220 Cov.: 32

Gnomad AFR AF: 0.151

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.326 AC: 49480 AN: 151890 Hom.: 9224 Cov.: 32 AF XY: 0.326 AC XY: 24207 AN XY: 74202

African (AFR) AF: 0.151 AC: 6272 AN: 41472

American (AMR) AF: 0.297 AC: 4524 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1144 AN: 3470

East Asian (EAS) AF: 0.321 AC: 1654 AN: 5160

South Asian (SAS) AF: 0.503 AC: 2424 AN: 4820

European-Finnish (FIN) AF: 0.378 AC: 3978 AN: 10514

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.419 AC: 28468 AN: 67906

Other (OTH) AF: 0.330 AC: 694 AN: 2102

Alfa AF: 0.403 Hom.: 10470

Bravo AF: 0.312

Asia WGS AF: 0.423 AC: 1473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.017
DANN	Benign	0.41
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs1431918; hg19: chr8-62885853; COSMIC: COSV69466666;