rs13186058

Variant names:

• chr5-151951269-G-A
• rs13186058
• ENST00000524295.5:n.156+233G>A

Variant summary

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

The ENST00000524295.5(LINC01933):​n.156+233G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 152,088 control chromosomes in the GnomAD database, including 3,753 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 0.20 (3753 hom., cov: 32)
• Consequence: LINC01933 ENST00000524295.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.818

Genes affected

LINC01933 (HGNC:52756): (long intergenic non-protein coding RNA 1933)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 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
LINC01933	ENST00000524295.5	n.156+233G>A		intron_variant	Intron 2 of 6	2

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30830 AN: 151970 Hom.: 3753 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.173

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.203 AC: 30831 AN: 152088 Hom.: 3753 Cov.: 32 AF XY: 0.198 AC XY: 14688 AN XY: 74348

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.288

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.110

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.209

Alfa AF: 0.255 Hom.: 7021

Bravo AF: 0.192

Asia WGS AF: 0.0680 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13186058; hg19: chr5-151330830;