8-128543917-A-G

Variant names:

• chr8-128543917-A-G
• rs6470637
• ENST00000520766.5:n.57+17153T>C

Variant summary

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

The NR_121672.1(LINC00824):​n.508+17153T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,244 control chromosomes in the GnomAD database, including 3,088 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 0.18 (3088 hom., cov: 33)
• Consequence: LINC00824 NR_121672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.369
• Publications: 10 publications found

Genes affected

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

ENSG00000298619 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.319 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_121672.1. 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.508+17153T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00824	ENST00000520766.5	TSL:5	n.57+17153T>C		intron	N/A
	LINC00824	ENST00000756796.1		n.424+17153T>C		intron	N/A
	LINC00824	ENST00000756797.1		n.425+17153T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.177 AC: 26920 AN: 152126 Hom.: 3084 Cov.: 33

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.106

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.177 AC: 26950 AN: 152244 Hom.: 3088 Cov.: 33 AF XY: 0.173 AC XY: 12903 AN XY: 74442

African (AFR) AF: 0.324 AC: 13439 AN: 41512

American (AMR) AF: 0.106 AC: 1615 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 378 AN: 3472

East Asian (EAS) AF: 0.0310 AC: 161 AN: 5186

South Asian (SAS) AF: 0.117 AC: 565 AN: 4822

European-Finnish (FIN) AF: 0.126 AC: 1333 AN: 10610

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8980 AN: 68032

Other (OTH) AF: 0.159 AC: 337 AN: 2114

Alfa AF: 0.125 Hom.: 950

Bravo AF: 0.182

Asia WGS AF: 0.0960 AC: 334 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.49
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6470637; hg19: chr8-129556163;