chr8-128465190-A-G

Position:

• chr8-128465190-A-G

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4 BA1

The NR_121672.1(LINC00824):​n.509-36806T>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 NR_121672.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.24

Genes affected

LINC00824 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.509-36806T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.58-36806T>C		intron_variant		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

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.0885

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.0250

Gnomad4 NFE AF: 0.0114

Gnomad4 OTH AF: 0.0781

Alfa AF: 0.0190 Hom.: 22

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6996647; hg19: chr8-129477436;