13-42391558-C-T

Variant names:

• chr13-42391558-C-T
• rs8001611
• ENST00000637462.1:n.440-2774C>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637462.1	n.440-2774C>T		intron_variant	Intron 3 of 7	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;