8-128554935-T-C

Position:

• chr8-128554935-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_121672.1(LINC00824):​n.508+6135A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,100 control chromosomes in the GnomAD database, including 3,232 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 0.18 (3232 hom., cov: 32)
• Consequence: LINC00824 NR_121672.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0870

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.508+6135A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC00824	ENST00000520766.5	n.57+6135A>G		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27462 AN: 151982 Hom.: 3230 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0914

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.109

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.116

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.181 AC: 27490 AN: 152100 Hom.: 3232 Cov.: 32 AF XY: 0.176 AC XY: 13122 AN XY: 74372

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.109

Gnomad4 EAS AF: 0.0282

Gnomad4 SAS AF: 0.116

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.164

Alfa AF: 0.136 Hom.: 3678

Bravo AF: 0.187

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	14
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: rs6651252; hg19: chr8-129567181;