rs13186058

Positions:

• chr5-151951269-G-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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01933	ENST00000524295.5	n.156+233G>A		intron_variant, non_coding_transcript_variant		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;