rs4958505

Variant names:

• chr5-151964493-A-G
• rs4958505
• ENST00000524034.6:n.95+5539A>G

Variant summary

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

The ENST00000524295.5(LINC01933):​n.199+12813A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,166 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 32)
• Consequence: LINC01933 ENST00000524295.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01933	NR_109876.1		n.57+5539A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01933	ENST00000524034.6	TSL:3	n.95+5539A>G		intron	N/A
	LINC01933	ENST00000524295.5	TSL:2	n.199+12813A>G		intron	N/A
	ENSG00000293808	ENST00000719158.1		n.242+16698A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32248 AN: 152048 Hom.: 4004 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.00307

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.212 AC: 32247 AN: 152166 Hom.: 4004 Cov.: 32 AF XY: 0.206 AC XY: 15308 AN XY: 74400

African (AFR) AF: 0.122 AC: 5075 AN: 41520

American (AMR) AF: 0.178 AC: 2719 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.279 AC: 970 AN: 3472

East Asian (EAS) AF: 0.00308 AC: 16 AN: 5194

South Asian (SAS) AF: 0.115 AC: 552 AN: 4814

European-Finnish (FIN) AF: 0.262 AC: 2771 AN: 10572

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.285 AC: 19375 AN: 67986

Other (OTH) AF: 0.215 AC: 455 AN: 2112

Alfa AF: 0.255 Hom.: 2961

Bravo AF: 0.202

Asia WGS AF: 0.0750 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.76
PhyloP100		0.81

Splicing

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

Other links and lift over

dbSNP: rs4958505; hg19: chr5-151344054;