rs273370

Variant names:

• chr5-5035083-G-A
• rs273370
• ENST00000508201.5:n.179+546G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000508201.5(LINC01020):​n.179+546G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,984 control chromosomes in the GnomAD database, including 51,090 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 0.80 (51090 hom., cov: 31)
• Consequence: LINC01020 ENST00000508201.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 1 publications found

Genes affected

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

ENSG00000251426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.907 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01020	NR_026994.1	n.179+546G>A		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01020	ENST00000508201.5	n.179+546G>A		intron_variant	Intron 1 of 7	1
LINC01020	ENST00000509382.5	n.75+546G>A		intron_variant	Intron 1 of 3	1
LINC01020	ENST00000507599.2	n.155+546G>A		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122241 AN: 151866 Hom.: 51092 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.990

Gnomad AMR AF: 0.881

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.860

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.930

Gnomad NFE AF: 0.913

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.804 AC: 122270 AN: 151984 Hom.: 51090 Cov.: 31 AF XY: 0.808 AC XY: 60004 AN XY: 74302

African (AFR) AF: 0.549 AC: 22703 AN: 41386

American (AMR) AF: 0.881 AC: 13470 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3182 AN: 3470

East Asian (EAS) AF: 0.859 AC: 4444 AN: 5172

South Asian (SAS) AF: 0.905 AC: 4350 AN: 4808

European-Finnish (FIN) AF: 0.869 AC: 9154 AN: 10540

Middle Eastern (MID) AF: 0.935 AC: 275 AN: 294

European-Non Finnish (NFE) AF: 0.913 AC: 62064 AN: 68004

Other (OTH) AF: 0.819 AC: 1725 AN: 2106

Alfa AF: 0.839 Hom.: 7123

Bravo AF: 0.792

Asia WGS AF: 0.819 AC: 2841 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.29
DANN	Benign	0.43
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs273370; hg19: chr5-5035196;