rs16903097

chr8-128544110-T-G

Variant summary

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

The NR_121672.1(LINC00824):n.508+16960A>C 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 0.164 in 152,156 control chromosomes in the GnomAD database, including 2,486 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 0.16 (2486 hom., cov: 32)
• Consequence: LINC00824 NR_121672.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.275 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00824	NR_121672.1	n.508+16960A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00824	ENST00000520766.5	n.57+16960A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24900 AN: 152038 Hom.: 2483 Cov.: 32

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.0923

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.0183

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.164 AC: 24929 AN: 152156 Hom.: 2486 Cov.: 32 AF XY: 0.160 AC XY: 11931 AN XY: 74394

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.0179

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.150

Alfa AF: 0.133 Hom.: 3072

Bravo AF: 0.168

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.47
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16903097; hg19: chr8-129556356;