13-42359719-T-C

Variant names:

• chr13-42359719-T-C
• rs238272
• ENST00000637462.1:n.229+17117T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637462.1(LINC02341):​n.229+17117T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,116 control chromosomes in the GnomAD database, including 37,693 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 (37693 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.45
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.844 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.229+17117T>C		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106788 AN: 151998 Hom.: 37667 Cov.: 33

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.658

Gnomad AMR AF: 0.763

Gnomad ASJ AF: 0.775

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.703

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.702 AC: 106861 AN: 152116 Hom.: 37693 Cov.: 33 AF XY: 0.707 AC XY: 52620 AN XY: 74396

African (AFR) AF: 0.652 AC: 27039 AN: 41478

American (AMR) AF: 0.763 AC: 11660 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.775 AC: 2690 AN: 3470

East Asian (EAS) AF: 0.865 AC: 4486 AN: 5184

South Asian (SAS) AF: 0.735 AC: 3552 AN: 4830

European-Finnish (FIN) AF: 0.688 AC: 7270 AN: 10560

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.703 AC: 47804 AN: 67996

Other (OTH) AF: 0.721 AC: 1522 AN: 2112

Alfa AF: 0.708 Hom.: 97343

Bravo AF: 0.707

Asia WGS AF: 0.788 AC: 2738 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.4
DANN	Benign	0.72
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs238272; hg19: chr13-42933855;