13-42391558-C-T

Variant names:

• chr13-42391558-C-T
• rs8001611
• ENST00000637462.1:n.440-2774C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 14 publications found

Genes affected

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637462.1	TSL:5	n.440-2774C>T		intron	N/A

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

African (AFR) AF: 0.669 AC: 27727 AN: 41472

American (AMR) AF: 0.596 AC: 9099 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2393 AN: 3468

East Asian (EAS) AF: 0.914 AC: 4744 AN: 5188

South Asian (SAS) AF: 0.718 AC: 3457 AN: 4818

European-Finnish (FIN) AF: 0.474 AC: 4988 AN: 10530

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.522 AC: 35488 AN: 67960

Other (OTH) AF: 0.596 AC: 1257 AN: 2110

Alfa AF: 0.548 Hom.: 31835

Bravo AF: 0.598

Asia WGS AF: 0.806 AC: 2802 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.44
DANN	Benign	0.22
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs8001611; hg19: chr13-42965694;