rs10520789

Variant names:

• chr15-95598638-G-A
• rs10520789
• ENST00000840569.1:n.145-11373G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000840569.1(LINC00924):​n.145-11373G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,286 control chromosomes in the GnomAD database, including 1,148 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 0.12 (1148 hom., cov: 33)
• Consequence: LINC00924 ENST00000840569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.50
• Publications: 15 publications found

Genes affected

LINC00924 (HGNC:27081): (long intergenic non-protein coding RNA 924)

ENSG00000309432 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.15).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00924	ENST00000840569.1	n.145-11373G>A		intron_variant	Intron 1 of 2
ENSG00000309432	ENST00000841104.1	n.327-3893C>T		intron_variant	Intron 2 of 4
ENSG00000309432	ENST00000841105.1	n.207-3893C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17559 AN: 152168 Hom.: 1149 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0905

Gnomad ASJ AF: 0.126

Gnomad EAS AF: 0.0254

Gnomad SAS AF: 0.0577

Gnomad FIN AF: 0.0415

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.106

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

GnomAD4 genome AF: 0.115 AC: 17561 AN: 152286 Hom.: 1148 Cov.: 33 AF XY: 0.109 AC XY: 8086 AN XY: 74454

African (AFR) AF: 0.158 AC: 6582 AN: 41554

American (AMR) AF: 0.0904 AC: 1382 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.126 AC: 438 AN: 3470

East Asian (EAS) AF: 0.0251 AC: 130 AN: 5186

South Asian (SAS) AF: 0.0582 AC: 281 AN: 4828

European-Finnish (FIN) AF: 0.0415 AC: 441 AN: 10614

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7967 AN: 68022

Other (OTH) AF: 0.105 AC: 222 AN: 2114

Alfa AF: 0.115 Hom.: 2337

Bravo AF: 0.120

Asia WGS AF: 0.0410 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.15
CADD	Benign	18
DANN	Benign	0.76
PhyloP100		3.5

Splicing

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

Other links and lift over

dbSNP: rs10520789; hg19: chr15-96141867;