chr8-128535888-A-G

Variant names:

• chr8-128535888-A-G
• rs1516974
• ENST00000520766.5:n.57+25182T>C

Variant summary

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

The ENST00000520766.5(LINC00824):​n.57+25182T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.141 in 152,144 control chromosomes in the GnomAD database, including 1,644 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 0.14 (1644 hom., cov: 32)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.02
• Publications: 8 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.508+25182T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.57+25182T>C		intron_variant	Intron 1 of 5	5
LINC00824	ENST00000756796.1	n.425-18985T>C		intron_variant	Intron 2 of 2
LINC00824	ENST00000756797.1	n.426-18985T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.141 AC: 21380 AN: 152026 Hom.: 1643 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.141 AC: 21396 AN: 152144 Hom.: 1644 Cov.: 32 AF XY: 0.138 AC XY: 10298 AN XY: 74376

African (AFR) AF: 0.199 AC: 8264 AN: 41504

American (AMR) AF: 0.0902 AC: 1379 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 377 AN: 3470

East Asian (EAS) AF: 0.0304 AC: 157 AN: 5170

South Asian (SAS) AF: 0.117 AC: 563 AN: 4814

European-Finnish (FIN) AF: 0.126 AC: 1331 AN: 10600

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8914 AN: 67984

Other (OTH) AF: 0.129 AC: 272 AN: 2116

Alfa AF: 0.125 Hom.: 206

Bravo AF: 0.140

Asia WGS AF: 0.0900 AC: 312 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.026
DANN	Benign	0.16
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs1516974; hg19: chr8-129548134;