13-42450574-C-T

Variant names:

• chr13-42450574-C-T
• rs9533108
• ENST00000637043.1:n.336+13102C>T

Variant summary

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

The ENST00000637043.1(LINC02341):​n.336+13102C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.442 in 152,020 control chromosomes in the GnomAD database, including 15,869 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 0.44 (15869 hom., cov: 32)
• Consequence: LINC02341 ENST00000637043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.938

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=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02341	NR_135319.1	n.336+13102C>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02341	ENST00000637043.1	n.336+13102C>T		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.443 AC: 67221 AN: 151902 Hom.: 15869 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.512

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.194

Gnomad SAS AF: 0.455

Gnomad FIN AF: 0.616

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.521

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.442 AC: 67232 AN: 152020 Hom.: 15869 Cov.: 32 AF XY: 0.446 AC XY: 33113 AN XY: 74324

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.195

Gnomad4 SAS AF: 0.455

Gnomad4 FIN AF: 0.616

Gnomad4 NFE AF: 0.521

Gnomad4 OTH AF: 0.432

Alfa AF: 0.490 Hom.: 8579

Bravo AF: 0.420

Asia WGS AF: 0.323 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.72
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9533108; hg19: chr13-43024710;