rs154111

Positions:

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

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_109876.1(LINC01933):​n.57+102880A>G 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 0.358 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 NR_109876.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

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=-0.9).
• 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/exons	MANE	Protein	UniProt
LINC01933	NR_109876.1	n.57+102880A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01933	ENST00000524295.5	n.199+110154A>G		intron_variant, non_coding_transcript_variant		2
LINC01933	ENST00000524034.6	n.95+102880A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.157

Gnomad4 AMR AF: 0.485

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.507

Gnomad4 SAS AF: 0.323

Gnomad4 FIN AF: 0.449

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.388

Alfa AF: 0.421 Hom.: 28465

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs154111; hg19: chr5-151441395;