rs344278

Positions:

• chr8-61956545-C-T

Variant summary

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

The XR_428354.4(LINC02842):​n.918-15679C>T 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 0.464 in 151,704 control chromosomes in the GnomAD database, including 16,637 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 (16637 hom., cov: 32)
• Consequence: LINC02842 XR_428354.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.75

Genes affected

LINC02842 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02842	XR_001745926.3	n.918-15679C>T		intron_variant, non_coding_transcript_variant
LINC02842	XR_007060925.1	n.875-15679C>T		intron_variant, non_coding_transcript_variant
LINC02842	XR_007060931.1	n.875-15679C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70417 AN: 151584 Hom.: 16632 Cov.: 32

Gnomad AFR AF: 0.400

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.412

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.558

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.460

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

GnomAD4 genome AF: 0.464 AC: 70447 AN: 151704 Hom.: 16637 Cov.: 32 AF XY: 0.463 AC XY: 34335 AN XY: 74104

Gnomad4 AFR AF: 0.399

Gnomad4 AMR AF: 0.411

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.557

Gnomad4 FIN AF: 0.485

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.467

Alfa AF: 0.479 Hom.: 2213

Bravo AF: 0.456

Asia WGS AF: 0.531 AC: 1847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.67
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs344278; hg19: chr8-62869104;