ENST00000520206.5:n.425-864T>C

Variant names:

• chr8-128415272-A-G
• rs7815944
• ENST00000520206.5:n.425-864T>C

Variant summary

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

The ENST00000520206.5(LINC00824):​n.425-864T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.118 in 151,710 control chromosomes in the GnomAD database, including 1,744 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 0.12 (1744 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: LINC00824 ENST00000520206.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 13 publications found

Genes affected

LINC00824 (HGNC:50281): (long intergenic non-protein coding RNA 824)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520206.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00824	NR_121672.1		n.1401-864T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00824	ENST00000520206.5	TSL:1	n.425-864T>C		intron	N/A
	LINC00824	ENST00000517583.1	TSL:5	n.16+94T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17810 AN: 151590 Hom.: 1739 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0427

Gnomad MID AF: 0.0701

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.102

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.118 AC: 17846 AN: 151710 Hom.: 1744 Cov.: 32 AF XY: 0.121 AC XY: 8946 AN XY: 74124

African (AFR) AF: 0.243 AC: 10061 AN: 41326

American (AMR) AF: 0.139 AC: 2113 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.0384 AC: 133 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1516 AN: 5156

South Asian (SAS) AF: 0.187 AC: 901 AN: 4810

European-Finnish (FIN) AF: 0.0427 AC: 449 AN: 10522

Middle Eastern (MID) AF: 0.0788 AC: 23 AN: 292

European-Non Finnish (NFE) AF: 0.0347 AC: 2354 AN: 67878

Other (OTH) AF: 0.104 AC: 220 AN: 2106

Alfa AF: 0.0714 Hom.: 2606

Bravo AF: 0.132

Asia WGS AF: 0.258 AC: 896 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.46
DANN	Benign	0.45
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs7815944; hg19: chr8-129427518;