rs17833323

Variant names:

• chr14-58878529-T-C
• rs17833323
• ENST00000553762.2:n.352+837T>C

Variant summary

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

The ENST00000553762.2(LINC01500):​n.352+837T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,152 control chromosomes in the GnomAD database, including 2,531 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 0.17 (2531 hom., cov: 32)
• Consequence: LINC01500 ENST00000553762.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.48
• Publications: 1 publications found

Genes affected

LINC01500 (HGNC:51166): (long intergenic non-protein coding RNA 1500)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000553762.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	NR_110547.1		n.269-15614T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01500	ENST00000553762.2	TSL:5	n.352+837T>C		intron	N/A
	LINC01500	ENST00000555378.5	TSL:3	n.269-15614T>C		intron	N/A
	LINC01500	ENST00000556815.6	TSL:3	n.295-15614T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26292 AN: 152034 Hom.: 2533 Cov.: 32

Gnomad AFR AF: 0.129

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0299

Gnomad SAS AF: 0.0570

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.174

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

GnomAD4 genome AF: 0.173 AC: 26286 AN: 152152 Hom.: 2531 Cov.: 32 AF XY: 0.172 AC XY: 12778 AN XY: 74380

African (AFR) AF: 0.129 AC: 5360 AN: 41528

American (AMR) AF: 0.150 AC: 2297 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 529 AN: 3470

East Asian (EAS) AF: 0.0301 AC: 156 AN: 5180

South Asian (SAS) AF: 0.0571 AC: 275 AN: 4820

European-Finnish (FIN) AF: 0.285 AC: 3009 AN: 10574

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13931 AN: 67978

Other (OTH) AF: 0.171 AC: 361 AN: 2114

Alfa AF: 0.183 Hom.: 438

Bravo AF: 0.163

Asia WGS AF: 0.0630 AC: 217 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.0050
DANN	Benign	0.60
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs17833323; hg19: chr14-59345247;