5-152188538-A-G

Variant names:

• chr5-152188538-A-G
• rs294958
• ENST00000518431.6:n.25-6903A>G

Variant summary

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

The ENST00000518431.6(LINC01933):​n.25-6903A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 152,042 control chromosomes in the GnomAD database, including 32,282 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 0.63 (32282 hom., cov: 32)
• Consequence: LINC01933 ENST00000518431.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01933	NR_109876.1	n.58-78727A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01933	ENST00000518431.6	n.25-6903A>G		intron_variant	Intron 1 of 3	3
LINC01933	ENST00000524034.6	n.96-78727A>G		intron_variant	Intron 1 of 2	3
LINC01933	ENST00000524295.5	n.200-6186A>G		intron_variant	Intron 3 of 6	2

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95972 AN: 151924 Hom.: 32209 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.608

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.499

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.566

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.632 AC: 96106 AN: 152042 Hom.: 32282 Cov.: 32 AF XY: 0.625 AC XY: 46458 AN XY: 74308

African (AFR) AF: 0.871 AC: 36126 AN: 41498

American (AMR) AF: 0.608 AC: 9288 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2128 AN: 3468

East Asian (EAS) AF: 0.624 AC: 3222 AN: 5162

South Asian (SAS) AF: 0.499 AC: 2406 AN: 4824

European-Finnish (FIN) AF: 0.429 AC: 4527 AN: 10548

Middle Eastern (MID) AF: 0.571 AC: 168 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36344 AN: 67958

Other (OTH) AF: 0.627 AC: 1322 AN: 2110

Alfa AF: 0.568 Hom.: 42110

Bravo AF: 0.658

Asia WGS AF: 0.637 AC: 2218 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.38

Splicing

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

Other links and lift over

dbSNP: rs294958; hg19: chr5-151568099;