rs168733

Variant names:

• chr5-4991059-A-G
• rs168733
• ENST00000509057.1:n.229-15799T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-4991059-A-G
• chr5-4991059-A-T

Variant summary

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

The ENST00000509057.1(ENSG00000250481):​n.229-15799T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 152,020 control chromosomes in the GnomAD database, including 20,128 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 0.48 (20128 hom., cov: 32)
• Consequence: ENSG00000250481 ENST00000509057.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.353

Genes affected

ENSG00000250481 (HGNC:):

LINC01020 (HGNC:27968): (long intergenic non-protein coding RNA 1020)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250481	ENST00000509057.1	n.229-15799T>C		intron_variant	Intron 2 of 3	3
LINC01020	ENST00000659550.1	n.204+3067A>G		intron_variant	Intron 1 of 1
ENSG00000250481	ENST00000667766.1	n.202-15799T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72765 AN: 151902 Hom.: 20076 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.388

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.416

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

GnomAD4 genome AF: 0.479 AC: 72869 AN: 152020 Hom.: 20128 Cov.: 32 AF XY: 0.475 AC XY: 35301 AN XY: 74294

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.388

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.365

Gnomad4 OTH AF: 0.420

Alfa AF: 0.428 Hom.: 2458

Bravo AF: 0.494

Asia WGS AF: 0.470 AC: 1630 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.1
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: rs168733; hg19: chr5-4991172;