8-128465190-A-G

Variant names:

• chr8-128465190-A-G
• rs6996647
• ENST00000520766.5:n.58-36806T>C

Variant summary

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

The ENST00000520766.5(LINC00824):​n.58-36806T>C variant causes a intron change. The variant allele was found at a frequency of 0.0879 in 152,162 control chromosomes in the GnomAD database, including 1,218 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 0.088 (1218 hom., cov: 32)
• Consequence: LINC00824 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.24
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.18).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.509-36806T>C		intron_variant	Intron 2 of 7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.58-36806T>C		intron_variant	Intron 1 of 5	5

Frequencies

GnomAD3 genomes AF: 0.0878 AC: 13345 AN: 152044 Hom.: 1210 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.00658

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.0758

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0114

Gnomad OTH AF: 0.0785

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

GnomAD4 genome AF: 0.0879 AC: 13370 AN: 152162 Hom.: 1218 Cov.: 32 AF XY: 0.0901 AC XY: 6701 AN XY: 74396

African (AFR) AF: 0.220 AC: 9116 AN: 41478

American (AMR) AF: 0.0885 AC: 1351 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0752 AC: 261 AN: 3472

East Asian (EAS) AF: 0.200 AC: 1037 AN: 5176

South Asian (SAS) AF: 0.0752 AC: 363 AN: 4824

European-Finnish (FIN) AF: 0.0250 AC: 265 AN: 10616

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.0114 AC: 773 AN: 68004

Other (OTH) AF: 0.0781 AC: 165 AN: 2112

Alfa AF: 0.0448 Hom.: 867

Bravo AF: 0.0955

Asia WGS AF: 0.161 AC: 558 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.18
CADD	Benign	21
DANN	Benign	0.76
PhyloP100		6.2

Splicing

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

Other links and lift over

dbSNP: rs6996647; hg19: chr8-129477436;