rs170020

Positions:

• chr5-151964997-G-A
• chr5-151964997-G-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+6043G>A 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 0.586 in 151,962 control chromosomes in the GnomAD database, including 26,934 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 0.59 (26934 hom., cov: 31)
• Consequence: LINC01933 NR_109876.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588

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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01933	NR_109876.1	n.57+6043G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01933	ENST00000524295.5	n.199+13317G>A		intron_variant, non_coding_transcript_variant		2
LINC01933	ENST00000524034.6	n.95+6043G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88990 AN: 151844 Hom.: 26903 Cov.: 31

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.524

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.603

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.547

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.577

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

GnomAD4 genome AF: 0.586 AC: 89073 AN: 151962 Hom.: 26934 Cov.: 31 AF XY: 0.582 AC XY: 43257 AN XY: 74268

Gnomad4 AFR AF: 0.734

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.603

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.578

Alfa AF: 0.540 Hom.: 51636

Bravo AF: 0.582

Asia WGS AF: 0.487 AC: 1691 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.61
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs170020; hg19: chr5-151344558;