rs9594738

Variant names:

• chr13-42378009-C-T
• rs9594738
• ENST00000637462.1:n.230-6248C>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.230-6248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 152,042 control chromosomes in the GnomAD database, including 12,666 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 0.39 (12666 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.224

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.474 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.230-6248C>T		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59378 AN: 151926 Hom.: 12666 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.0840

Gnomad SAS AF: 0.280

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.478

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.391 AC: 59391 AN: 152042 Hom.: 12666 Cov.: 32 AF XY: 0.389 AC XY: 28876 AN XY: 74296

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.310

Gnomad4 EAS AF: 0.0840

Gnomad4 SAS AF: 0.280

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.478

Gnomad4 OTH AF: 0.389

Alfa AF: 0.449 Hom.: 33954

Bravo AF: 0.380

Asia WGS AF: 0.186 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.2
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: rs9594738; hg19: chr13-42952145;