rs1516982

Variant names:

• chr8-128521400-A-G
• rs1516982
• ENST00000520766.5:n.57+39670T>C

Variant summary

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

The ENST00000520766.5(LINC00824):​n.57+39670T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,054 control chromosomes in the GnomAD database, including 1,891 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 0.15 (1891 hom., cov: 32)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.542
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.508+39670T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.57+39670T>C		intron_variant	Intron 1 of 5	5
LINC00824	ENST00000756796.1	n.425-4497T>C		intron_variant	Intron 2 of 2
LINC00824	ENST00000756797.1	n.426-4497T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23328 AN: 151936 Hom.: 1887 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.0588

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.142

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.147

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

GnomAD4 genome AF: 0.154 AC: 23363 AN: 152054 Hom.: 1891 Cov.: 32 AF XY: 0.152 AC XY: 11290 AN XY: 74358

African (AFR) AF: 0.184 AC: 7624 AN: 41458

American (AMR) AF: 0.117 AC: 1790 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0945 AC: 328 AN: 3472

East Asian (EAS) AF: 0.0588 AC: 303 AN: 5156

South Asian (SAS) AF: 0.127 AC: 610 AN: 4818

European-Finnish (FIN) AF: 0.142 AC: 1501 AN: 10588

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.158 AC: 10730 AN: 67956

Other (OTH) AF: 0.148 AC: 313 AN: 2114

Alfa AF: 0.157 Hom.: 6191

Bravo AF: 0.155

Asia WGS AF: 0.103 AC: 359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.98
DANN	Benign	0.57
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs1516982; hg19: chr8-129533646;