rs344214

chr8-62024600-G-Achr8-62024600-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_928962.3(LINC02842):n.1151-18322G>A variant causes a intron, non coding transcript 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 XR_928962.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08

Genes affected

LINC02842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02842	XR_928962.3	n.1151-18322G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.912

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.541

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.687

Gnomad4 FIN AF: 0.590

Gnomad4 NFE AF: 0.628

Gnomad4 OTH AF: 0.694

Alfa AF: 0.654 Hom.: 3933

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344214; hg19: chr8-62937159;