13-42340510-G-T

Variant names:

• chr13-42340510-G-T
• rs238250
• ENST00000637462.1:n.107+1216G>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.107+1216G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,956 control chromosomes in the GnomAD database, including 2,387 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 0.17 (2387 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

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 (AFR) allele frequency at 95% confidence interval = 0.248 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.107+1216G>T		intron_variant	Intron 1 of 7	5

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25355 AN: 151838 Hom.: 2386 Cov.: 32

Gnomad AFR AF: 0.253

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.0844

Gnomad ASJ AF: 0.0874

Gnomad EAS AF: 0.0486

Gnomad SAS AF: 0.0983

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.167 AC: 25374 AN: 151956 Hom.: 2387 Cov.: 32 AF XY: 0.165 AC XY: 12228 AN XY: 74262

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.0842

Gnomad4 ASJ AF: 0.0874

Gnomad4 EAS AF: 0.0483

Gnomad4 SAS AF: 0.0984

Gnomad4 FIN AF: 0.210

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.146

Alfa AF: 0.136 Hom.: 1521

Bravo AF: 0.160

Asia WGS AF: 0.0870 AC: 304 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	0.52
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238250; hg19: chr13-42914646;