rs154111

Variant names:

• chr5-152061834-A-G
• rs154111
• ENST00000524034.6:n.95+102880A>G

Your query was ambiguous. Multiple possible variants found:

• chr5-152061834-A-G
• chr5-152061834-A-T

Variant summary

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

The ENST00000524034.6(LINC01933):​n.95+102880A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,202 control chromosomes in the GnomAD database, including 11,088 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 0.36 (11088 hom., cov: 33)
• Consequence: LINC01933 ENST00000524034.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18
• Publications: 3 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 (EAS) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01933	NR_109876.1	n.57+102880A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01933	ENST00000524034.6	n.95+102880A>G		intron_variant	Intron 1 of 2	3
LINC01933	ENST00000524295.5	n.199+110154A>G		intron_variant	Intron 3 of 6	2

Frequencies

GnomAD3 genomes AF: 0.358 AC: 54430 AN: 152084 Hom.: 11088 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.484

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.507

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.449

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.358 AC: 54438 AN: 152202 Hom.: 11088 Cov.: 33 AF XY: 0.362 AC XY: 26925 AN XY: 74424

African (AFR) AF: 0.157 AC: 6505 AN: 41556

American (AMR) AF: 0.485 AC: 7410 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1496 AN: 3472

East Asian (EAS) AF: 0.507 AC: 2618 AN: 5166

South Asian (SAS) AF: 0.323 AC: 1559 AN: 4822

European-Finnish (FIN) AF: 0.449 AC: 4754 AN: 10594

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28796 AN: 67990

Other (OTH) AF: 0.388 AC: 821 AN: 2114

Alfa AF: 0.410 Hom.: 57363

Bravo AF: 0.356

Asia WGS AF: 0.386 AC: 1342 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.69
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs154111; hg19: chr5-151441395;