ENST00000716893.1:n.523+5033A>G

Variant names:

• chr20-50176825-A-G
• rs2869961
• ENST00000716893.1:n.523+5033A>G

Variant summary

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

The ENST00000716893.1(LINC01273):​n.523+5033A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.921 in 152,126 control chromosomes in the GnomAD database, including 64,636 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 0.92 (64636 hom., cov: 30)
• Consequence: LINC01273 ENST00000716893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.229
• Publications: 2 publications found

Genes affected

LINC01273 (HGNC:50329): (long intergenic non-protein coding RNA 1273)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.06).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.977 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716893.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01273	NR_109943.1		n.*154A>G		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01273	ENST00000716893.1		n.523+5033A>G		intron	N/A
	LINC01273	ENST00000411453.4	TSL:2	n.*148A>G		downstream_gene	N/A
	LINC01273	ENST00000659473.1		n.*153A>G		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.921 AC: 139999 AN: 152008 Hom.: 64570 Cov.: 30

Gnomad AFR AF: 0.977

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.839

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.977

Gnomad FIN AF: 0.906

Gnomad MID AF: 0.898

Gnomad NFE AF: 0.884

Gnomad OTH AF: 0.902

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

GnomAD4 genome AF: 0.921 AC: 140124 AN: 152126 Hom.: 64636 Cov.: 30 AF XY: 0.923 AC XY: 68625 AN XY: 74354

African (AFR) AF: 0.977 AC: 40557 AN: 41506

American (AMR) AF: 0.923 AC: 14091 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.839 AC: 2910 AN: 3468

East Asian (EAS) AF: 1.00 AC: 5178 AN: 5178

South Asian (SAS) AF: 0.977 AC: 4710 AN: 4820

European-Finnish (FIN) AF: 0.906 AC: 9588 AN: 10582

Middle Eastern (MID) AF: 0.901 AC: 263 AN: 292

European-Non Finnish (NFE) AF: 0.884 AC: 60107 AN: 68000

Other (OTH) AF: 0.904 AC: 1905 AN: 2108

Alfa AF: 0.905 Hom.: 42879

Bravo AF: 0.923

Asia WGS AF: 0.985 AC: 3427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.6
DANN	Benign	0.23
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs2869961; hg19: chr20-48793362;