8-128555832-C-T

Variant names:

• chr8-128555832-C-T
• rs1561927
• ENST00000520766.5:n.57+5238G>A

Variant summary

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

The ENST00000520766.5(LINC00824):​n.57+5238G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,186 control chromosomes in the GnomAD database, including 34,742 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 0.66 (34742 hom., cov: 34)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.930
• Publications: 54 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.508+5238G>A		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.57+5238G>A		intron_variant	Intron 1 of 5	5
LINC00824	ENST00000756796.1	n.424+5238G>A		intron_variant	Intron 2 of 2
LINC00824	ENST00000756797.1	n.425+5238G>A		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.658 AC: 100004 AN: 152068 Hom.: 34735 Cov.: 34

Gnomad AFR AF: 0.420

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.703

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.639

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.657 AC: 100043 AN: 152186 Hom.: 34742 Cov.: 34 AF XY: 0.661 AC XY: 49207 AN XY: 74398

African (AFR) AF: 0.420 AC: 17428 AN: 41508

American (AMR) AF: 0.780 AC: 11925 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.709 AC: 2461 AN: 3470

East Asian (EAS) AF: 0.969 AC: 5022 AN: 5184

South Asian (SAS) AF: 0.703 AC: 3396 AN: 4830

European-Finnish (FIN) AF: 0.728 AC: 7702 AN: 10578

Middle Eastern (MID) AF: 0.629 AC: 185 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49838 AN: 68004

Other (OTH) AF: 0.692 AC: 1461 AN: 2112

Alfa AF: 0.711 Hom.: 150530

Bravo AF: 0.651

Asia WGS AF: 0.795 AC: 2766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.30
DANN	Benign	0.65
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs1561927; hg19: chr8-129568078;