rs17798800

Variant names:

• chr13-34376390-C-T
• rs17798800
• ENST00000605909.1:n.82+28266C>T

Variant summary

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

The ENST00000605909.1(LINC02343):​n.82+28266C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,056 control chromosomes in the GnomAD database, including 2,727 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 0.19 (2727 hom., cov: 32)
• Consequence: LINC02343 ENST00000605909.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 10 publications found

Genes affected

LINC02343 (HGNC:53263): (long intergenic non-protein coding RNA 2343)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02343	NR_146542.1	n.82+28266C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02343	ENST00000605909.1	n.82+28266C>T		intron_variant	Intron 1 of 3	4
LINC02343	ENST00000664334.1	n.139+28266C>T		intron_variant	Intron 1 of 2
LINC02343	ENST00000791005.1	n.85+28266C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28170 AN: 151936 Hom.: 2722 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.171

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

GnomAD4 genome AF: 0.185 AC: 28180 AN: 152056 Hom.: 2727 Cov.: 32 AF XY: 0.185 AC XY: 13764 AN XY: 74328

African (AFR) AF: 0.187 AC: 7732 AN: 41454

American (AMR) AF: 0.136 AC: 2073 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 506 AN: 3468

East Asian (EAS) AF: 0.137 AC: 711 AN: 5186

South Asian (SAS) AF: 0.210 AC: 1014 AN: 4822

European-Finnish (FIN) AF: 0.200 AC: 2109 AN: 10558

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13433 AN: 67968

Other (OTH) AF: 0.173 AC: 364 AN: 2106

Alfa AF: 0.190 Hom.: 5682

Bravo AF: 0.178

Asia WGS AF: 0.174 AC: 605 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs17798800; hg19: chr13-34950527;