rs10505517

Variant names:

• chr8-128465765-A-G
• rs10505517
• ENST00000520766.5:n.58-37381T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_121672.1(LINC00824):​n.509-37381T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 152,076 control chromosomes in the GnomAD database, including 7,141 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 0.24 (7141 hom., cov: 32)
• Consequence: LINC00824 NR_121672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0240

Genes affected

LINC00824 (HGNC:50281): (long intergenic non-protein coding RNA 824)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.526 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.509-37381T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.58-37381T>C		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36031 AN: 151958 Hom.: 7118 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.0891

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.237 AC: 36108 AN: 152076 Hom.: 7141 Cov.: 32 AF XY: 0.239 AC XY: 17803 AN XY: 74346

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.175

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.317

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.0699

Gnomad4 NFE AF: 0.0891

Gnomad4 OTH AF: 0.205

Alfa AF: 0.123 Hom.: 2640

Bravo AF: 0.253

Asia WGS AF: 0.354 AC: 1227 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.5
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505517; hg19: chr8-129478011;