13-42423131-C-T

Variant names:

• chr13-42423131-C-T
• rs9594751
• ENST00000637462.1:n.868+11079C>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.868+11079C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,062 control chromosomes in the GnomAD database, including 2,492 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 0.16 (2492 hom., cov: 33)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 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.868+11079C>T		intron_variant	Intron 5 of 7	5

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24080 AN: 151944 Hom.: 2493 Cov.: 33

Gnomad AFR AF: 0.0373

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.106

Gnomad EAS AF: 0.0617

Gnomad SAS AF: 0.151

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.128

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

GnomAD4 genome AF: 0.158 AC: 24072 AN: 152062 Hom.: 2492 Cov.: 33 AF XY: 0.159 AC XY: 11810 AN XY: 74322

Gnomad4 AFR AF: 0.0372

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.106

Gnomad4 EAS AF: 0.0613

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.126

Alfa AF: 0.199 Hom.: 6786

Bravo AF: 0.150

Asia WGS AF: 0.0890 AC: 307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9594751; hg19: chr13-42997267;