rs9525613

Variant names:

• chr13-42344512-C-T
• rs9525613
• ENST00000637462.1:n.229+1910C>T

Variant summary

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

The ENST00000637462.1(LINC02341):​n.229+1910C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,068 control chromosomes in the GnomAD database, including 5,799 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 0.27 (5799 hom., cov: 32)
• Consequence: LINC02341 ENST00000637462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141
• Publications: 7 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.291 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.229+1910C>T		intron_variant	Intron 2 of 7	5

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41625 AN: 151950 Hom.: 5796 Cov.: 32

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.221

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.280

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.274 AC: 41651 AN: 152068 Hom.: 5799 Cov.: 32 AF XY: 0.270 AC XY: 20062 AN XY: 74338

African (AFR) AF: 0.296 AC: 12255 AN: 41462

American (AMR) AF: 0.221 AC: 3372 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.228 AC: 791 AN: 3466

East Asian (EAS) AF: 0.137 AC: 709 AN: 5176

South Asian (SAS) AF: 0.268 AC: 1291 AN: 4812

European-Finnish (FIN) AF: 0.308 AC: 3258 AN: 10574

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.280 AC: 19039 AN: 67976

Other (OTH) AF: 0.269 AC: 568 AN: 2110

Alfa AF: 0.279 Hom.: 3265

Bravo AF: 0.267

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.4
DANN	Benign	0.47
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs9525613; hg19: chr13-42918648;