rs9525613

chr13-42344512-C-T

Variant summary

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

The ENST00000637462.1(LINC02341):n.229+1910C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

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=-0.91).
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02341	ENST00000637462.1	n.229+1910C>T		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.296

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.280

Gnomad4 OTH AF: 0.269

Alfa AF: 0.279 Hom.: 2940

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9525613; hg19: chr13-42918648;