rs170020

Variant names:

• chr5-151964997-G-A
• rs170020
• ENST00000524034.6:n.95+6043G>A

Your query was ambiguous. Multiple possible variants found:

• chr5-151964997-G-A
• chr5-151964997-G-C
• chr5-151964997-G-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+6043G>A variant causes a intron 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 ENST00000524034.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 11 publications found

Genes affected

LINC01933 (HGNC:52756): (long intergenic non-protein coding RNA 1933)

ENSG00000293808 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC01933	NR_109876.1	n.57+6043G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01933	ENST00000524034.6	n.95+6043G>A		intron_variant	Intron 1 of 2	3
LINC01933	ENST00000524295.5	n.199+13317G>A		intron_variant	Intron 3 of 6	2
ENSG00000293808	ENST00000719158.1	n.242+17202G>A		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.734 AC: 30418 AN: 41432

American (AMR) AF: 0.480 AC: 7338 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.603 AC: 2092 AN: 3468

East Asian (EAS) AF: 0.334 AC: 1722 AN: 5152

South Asian (SAS) AF: 0.547 AC: 2632 AN: 4812

European-Finnish (FIN) AF: 0.572 AC: 6026 AN: 10536

Middle Eastern (MID) AF: 0.531 AC: 156 AN: 294

European-Non Finnish (NFE) AF: 0.544 AC: 36992 AN: 67970

Other (OTH) AF: 0.578 AC: 1220 AN: 2112

Alfa AF: 0.548 Hom.: 105086

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
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs170020; hg19: chr5-151344558;