ENST00000637462.1:n.229+17117T>C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-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

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.763

Gnomad4 ASJ AF: 0.775

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.735

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.703

Gnomad4 OTH AF: 0.721

Alfa AF: 0.699 Hom.: 3608

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238272; hg19: chr13-42933855;