13-42391558-C-T

Variant summary

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

The ENST00000637462.1(LINC02341):n.440-2774C>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 0.59 in 152,024 control chromosomes in the GnomAD database, including 27,284 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 0.59 (27284 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.746

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

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 (EAS) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02341	ENST00000637462.1	n.440-2774C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.590 AC: 89667 AN: 151904 Hom.: 27246 Cov.: 32

Gnomad AFR AF: 0.669

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.595

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.573

Gnomad NFE AF: 0.522

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.590 AC: 89763 AN: 152024 Hom.: 27284 Cov.: 32 AF XY: 0.593 AC XY: 44071 AN XY: 74306

Gnomad4 AFR AF: 0.669

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.690

Gnomad4 EAS AF: 0.914

Gnomad4 SAS AF: 0.718

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.522

Gnomad4 OTH AF: 0.596

Alfa AF: 0.543 Hom.: 2854

Bravo AF: 0.598

Asia WGS AF: 0.806 AC: 2802 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.44
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8001611; hg19: chr13-42965694;