13-42423131-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000637462.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02341	ENST00000637462.1	TSL:5	n.868+11079C>T		intron	N/A

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

African (AFR) AF: 0.0372 AC: 1542 AN: 41472

American (AMR) AF: 0.199 AC: 3042 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.106 AC: 368 AN: 3472

East Asian (EAS) AF: 0.0613 AC: 318 AN: 5190

South Asian (SAS) AF: 0.151 AC: 727 AN: 4806

European-Finnish (FIN) AF: 0.249 AC: 2631 AN: 10558

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14926 AN: 67962

Other (OTH) AF: 0.126 AC: 266 AN: 2112

Alfa AF: 0.192 Hom.: 9704

Bravo AF: 0.150

Asia WGS AF: 0.0890 AC: 307 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.66
DANN	Benign	0.49
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs9594751; hg19: chr13-42997267;