rs13186058

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ENSG00000293808 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000524295.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01933	ENST00000524295.5	TSL:2	n.156+233G>A		intron	N/A
	ENSG00000293808	ENST00000719158.1		n.242+3474G>A		intron	N/A

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

African (AFR) AF: 0.103 AC: 4288 AN: 41488

American (AMR) AF: 0.173 AC: 2641 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 998 AN: 3470

East Asian (EAS) AF: 0.00289 AC: 15 AN: 5182

South Asian (SAS) AF: 0.110 AC: 533 AN: 4824

European-Finnish (FIN) AF: 0.261 AC: 2766 AN: 10578

Middle Eastern (MID) AF: 0.252 AC: 74 AN: 294

European-Non Finnish (NFE) AF: 0.277 AC: 18838 AN: 67948

Other (OTH) AF: 0.209 AC: 441 AN: 2110

Alfa AF: 0.250 Hom.: 8625

Bravo AF: 0.192

Asia WGS AF: 0.0680 AC: 240 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	7.2
DANN	Benign	0.73
PhyloP100		0.82

Splicing

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

Other links and lift over

dbSNP: rs13186058; hg19: chr5-151330830;