chr8-128468291-A-G

Variant names:

• chr8-128468291-A-G
• rs10505516
• ENST00000520766.5:n.58-39907T>C

Variant summary

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

The ENST00000520766.5(LINC00824):​n.58-39907T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 148,886 control chromosomes in the GnomAD database, including 2,391 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 (2391 hom., cov: 28)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230
• Publications: 1 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.509-39907T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.58-39907T>C		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21356 AN: 148796 Hom.: 2382 Cov.: 28

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.0824

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.144 AC: 21394 AN: 148886 Hom.: 2391 Cov.: 28 AF XY: 0.143 AC XY: 10382 AN XY: 72514

African (AFR) AF: 0.297 AC: 11863 AN: 39876

American (AMR) AF: 0.0825 AC: 1236 AN: 14984

Ashkenazi Jewish (ASJ) AF: 0.109 AC: 376 AN: 3462

East Asian (EAS) AF: 0.131 AC: 663 AN: 5080

South Asian (SAS) AF: 0.272 AC: 1282 AN: 4718

European-Finnish (FIN) AF: 0.0360 AC: 355 AN: 9856

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 290

European-Non Finnish (NFE) AF: 0.0772 AC: 5222 AN: 67628

Other (OTH) AF: 0.123 AC: 257 AN: 2082

Alfa AF: 0.112 Hom.: 205

Bravo AF: 0.155

Asia WGS AF: 0.197 AC: 684 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		-0.23

Splicing

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

Other links and lift over

dbSNP: rs10505516; hg19: chr8-129480537;