rs10098821

Variant names:

• chr8-128546982-C-T
• rs10098821
• ENST00000520766.5:n.57+14088G>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+14088G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0759 in 150,122 control chromosomes in the GnomAD database, including 561 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 0.076 (561 hom., cov: 31)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175
• Publications: 12 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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.508+14088G>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+14088G>A		intron_variant	Intron 1 of 5	5
LINC00824	ENST00000756796.1	n.424+14088G>A		intron_variant	Intron 2 of 2
LINC00824	ENST00000756797.1	n.425+14088G>A		intron_variant	Intron 2 of 3
ENSG00000298619	ENST00000756966.1	n.84+3277C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0759 AC: 11389 AN: 150016 Hom.: 562 Cov.: 31

Gnomad AFR AF: 0.0248

Gnomad AMI AF: 0.0861

Gnomad AMR AF: 0.0600

Gnomad ASJ AF: 0.0779

Gnomad EAS AF: 0.00472

Gnomad SAS AF: 0.0625

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0759 AC: 11389 AN: 150122 Hom.: 561 Cov.: 31 AF XY: 0.0746 AC XY: 5462 AN XY: 73184

African (AFR) AF: 0.0248 AC: 1011 AN: 40838

American (AMR) AF: 0.0598 AC: 899 AN: 15032

Ashkenazi Jewish (ASJ) AF: 0.0779 AC: 270 AN: 3466

East Asian (EAS) AF: 0.00473 AC: 24 AN: 5074

South Asian (SAS) AF: 0.0632 AC: 302 AN: 4776

European-Finnish (FIN) AF: 0.108 AC: 1080 AN: 9958

Middle Eastern (MID) AF: 0.148 AC: 42 AN: 284

European-Non Finnish (NFE) AF: 0.111 AC: 7517 AN: 67698

Other (OTH) AF: 0.0794 AC: 166 AN: 2090

Alfa AF: 0.0944 Hom.: 599

Bravo AF: 0.0712

Asia WGS AF: 0.0270 AC: 95 AN: 3454

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.7
DANN	Benign	0.42
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs10098821; hg19: chr8-129559228;