rs294958

Positions:

• chr5-152188538-A-G

Variant summary

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

The NR_109876.1(LINC01933):​n.58-78727A>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 0.632 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 NR_109876.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.384

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 (AFR) allele frequency at 95% confidence interval = 0.863 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01933	NR_109876.1	n.58-78727A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01933	ENST00000524295.5	n.200-6186A>G		intron_variant, non_coding_transcript_variant		2
LINC01933	ENST00000524034.6	n.96-78727A>G		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.871

Gnomad4 AMR AF: 0.608

Gnomad4 ASJ AF: 0.614

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.499

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.627

Alfa AF: 0.555 Hom.: 31364

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs294958; hg19: chr5-151568099;