13-42458457-C-T

Variant names:

• chr13-42458457-C-T
• rs9594759
• ENST00000637043.2:n.336+20985C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000637043.2(LINC02341):​n.336+20985C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 152,008 control chromosomes in the GnomAD database, including 19,806 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 0.51 (19806 hom., cov: 33)
• Consequence: LINC02341 ENST00000637043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0400
• Publications: 62 publications found

Genes affected

LINC02341 (HGNC:53261): (long intergenic non-protein coding RNA 2341)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637043.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	NR_135319.1		n.336+20985C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637043.2	TSL:3	n.336+20985C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.505 AC: 76737 AN: 151890 Hom.: 19791 Cov.: 33

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.236

Gnomad SAS AF: 0.478

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.541

Gnomad OTH AF: 0.486

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

GnomAD4 genome AF: 0.505 AC: 76789 AN: 152008 Hom.: 19806 Cov.: 33 AF XY: 0.508 AC XY: 37720 AN XY: 74302

African (AFR) AF: 0.476 AC: 19714 AN: 41442

American (AMR) AF: 0.456 AC: 6964 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1534 AN: 3468

East Asian (EAS) AF: 0.237 AC: 1226 AN: 5170

South Asian (SAS) AF: 0.478 AC: 2303 AN: 4822

European-Finnish (FIN) AF: 0.629 AC: 6639 AN: 10548

Middle Eastern (MID) AF: 0.606 AC: 177 AN: 292

European-Non Finnish (NFE) AF: 0.541 AC: 36741 AN: 67964

Other (OTH) AF: 0.485 AC: 1026 AN: 2114

Alfa AF: 0.517 Hom.: 79271

Bravo AF: 0.489

Asia WGS AF: 0.368 AC: 1279 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	12
DANN	Benign	0.82
PhyloP100		-0.040

Splicing

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

Other links and lift over

dbSNP: rs9594759; hg19: chr13-43032593;