8-128525500-G-C

Variant names:

• chr8-128525500-G-C
• rs17232730
• ENST00000520766.5:n.57+35570C>G

Variant summary

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

The ENST00000520766.5(LINC00824):​n.57+35570C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0972 in 151,896 control chromosomes in the GnomAD database, including 804 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 0.097 (804 hom., cov: 32)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.479
• Publications: 3 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.122 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000520766.5. 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
	LINC00824	NR_121672.1		n.508+35570C>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00824	ENST00000520766.5	TSL:5	n.57+35570C>G		intron	N/A
	LINC00824	ENST00000756796.1		n.425-8597C>G		intron	N/A
	LINC00824	ENST00000756797.1		n.426-8597C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14757 AN: 151778 Hom.: 804 Cov.: 32

Gnomad AFR AF: 0.0740

Gnomad AMI AF: 0.0866

Gnomad AMR AF: 0.0745

Gnomad ASJ AF: 0.0994

Gnomad EAS AF: 0.00406

Gnomad SAS AF: 0.0619

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.110

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

GnomAD4 genome AF: 0.0972 AC: 14765 AN: 151896 Hom.: 804 Cov.: 32 AF XY: 0.0950 AC XY: 7051 AN XY: 74212

African (AFR) AF: 0.0740 AC: 3063 AN: 41414

American (AMR) AF: 0.0742 AC: 1131 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0994 AC: 345 AN: 3470

East Asian (EAS) AF: 0.00407 AC: 21 AN: 5156

South Asian (SAS) AF: 0.0625 AC: 301 AN: 4814

European-Finnish (FIN) AF: 0.108 AC: 1135 AN: 10544

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8415 AN: 67952

Other (OTH) AF: 0.110 AC: 231 AN: 2106

Alfa AF: 0.0479 Hom.: 41

Bravo AF: 0.0959

Asia WGS AF: 0.0320 AC: 113 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.44
DANN	Benign	0.60
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs17232730; hg19: chr8-129537746;