5-151964493-A-G

Position:

• chr5-151964493-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.57+5539A>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 0.212 in 152,166 control chromosomes in the GnomAD database, including 4,004 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 0.21 (4004 hom., cov: 32)
• Consequence: LINC01933 NR_109876.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814

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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01933	NR_109876.1	n.57+5539A>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+12813A>G		intron_variant, non_coding_transcript_variant		2
LINC01933	ENST00000524034.6	n.95+5539A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32248 AN: 152048 Hom.: 4004 Cov.: 32

Gnomad AFR AF: 0.122

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.279

Gnomad EAS AF: 0.00307

Gnomad SAS AF: 0.114

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.285

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.212 AC: 32247 AN: 152166 Hom.: 4004 Cov.: 32 AF XY: 0.206 AC XY: 15308 AN XY: 74400

Gnomad4 AFR AF: 0.122

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.279

Gnomad4 EAS AF: 0.00308

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.285

Gnomad4 OTH AF: 0.215

Alfa AF: 0.254 Hom.: 2631

Bravo AF: 0.202

Asia WGS AF: 0.0750 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.4
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4958505; hg19: chr5-151344054;