rs154104

Variant names:

• chr5-152102169-A-G
• rs154104
• ENST00000518431.6:n.24+6594A>G

Variant summary

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

The ENST00000518431.6(LINC01933):​n.24+6594A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,108 control chromosomes in the GnomAD database, including 2,196 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 0.15 (2196 hom., cov: 32)
• Consequence: LINC01933 ENST00000518431.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.215 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01933	NR_109876.1	n.57+143215A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01933	ENST00000518431.6	n.24+6594A>G		intron_variant	Intron 1 of 3	3
LINC01933	ENST00000524034.6	n.95+143215A>G		intron_variant	Intron 1 of 2	3
LINC01933	ENST00000524295.5	n.200-92555A>G		intron_variant	Intron 3 of 6	2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22350 AN: 151990 Hom.: 2196 Cov.: 32

Gnomad AFR AF: 0.0477

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.218

Gnomad OTH AF: 0.175

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

GnomAD4 genome AF: 0.147 AC: 22351 AN: 152108 Hom.: 2196 Cov.: 32 AF XY: 0.141 AC XY: 10494 AN XY: 74350

African (AFR) AF: 0.0477 AC: 1979 AN: 41506

American (AMR) AF: 0.160 AC: 2440 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 725 AN: 3466

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5180

South Asian (SAS) AF: 0.0776 AC: 374 AN: 4822

European-Finnish (FIN) AF: 0.135 AC: 1431 AN: 10584

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.218 AC: 14826 AN: 67960

Other (OTH) AF: 0.173 AC: 366 AN: 2114

Alfa AF: 0.165 Hom.: 453

Bravo AF: 0.145

Asia WGS AF: 0.0530 AC: 185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.76
PhyloP100		-0.063
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs154104; hg19: chr5-151481730;