rs344214

Variant names:

• chr8-62024600-G-A
• rs344214
• ENST00000715768.1:n.706-18322G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-62024600-G-A
• chr8-62024600-G-T

Variant summary

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

The ENST00000715768.1(LINC02842):​n.706-18322G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.704 in 152,104 control chromosomes in the GnomAD database, including 39,196 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 0.70 (39196 hom., cov: 32)
• Consequence: LINC02842 ENST00000715768.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.904 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.706-18322G>A		intron_variant	Intron 6 of 10
LINC02842	ENST00000850662.1	n.434+37196G>A		intron_variant	Intron 3 of 6

Frequencies

GnomAD3 genomes AF: 0.704 AC: 107053 AN: 151984 Hom.: 39151 Cov.: 32

Gnomad AFR AF: 0.912

Gnomad AMI AF: 0.720

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.746

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.688

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

GnomAD4 genome AF: 0.704 AC: 107150 AN: 152104 Hom.: 39196 Cov.: 32 AF XY: 0.700 AC XY: 52015 AN XY: 74336

African (AFR) AF: 0.912 AC: 37890 AN: 41546

American (AMR) AF: 0.589 AC: 8983 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1878 AN: 3472

East Asian (EAS) AF: 0.746 AC: 3860 AN: 5172

South Asian (SAS) AF: 0.687 AC: 3310 AN: 4816

European-Finnish (FIN) AF: 0.590 AC: 6226 AN: 10548

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42714 AN: 67980

Other (OTH) AF: 0.694 AC: 1462 AN: 2108

Alfa AF: 0.665 Hom.: 4251

Bravo AF: 0.714

Asia WGS AF: 0.734 AC: 2557 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	7.5
DANN	Benign	0.58
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs344214; hg19: chr8-62937159;