rs16903097

Variant names:

• chr8-128544110-T-G
• rs16903097
• ENST00000520766.5:n.57+16960A>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+16960A>C variant causes a intron 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 ENST00000520766.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.927
• Publications: 11 publications found

Genes affected

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

ENSG00000298619 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LINC00824	NR_121672.1	n.508+16960A>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+16960A>C		intron_variant	Intron 1 of 5	5
LINC00824	ENST00000756796.1	n.424+16960A>C		intron_variant	Intron 2 of 2
LINC00824	ENST00000756797.1	n.425+16960A>C		intron_variant	Intron 2 of 3
ENSG00000298619	ENST00000756966.1	n.84+405T>G		intron_variant	Intron 1 of 1

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

African (AFR) AF: 0.279 AC: 11578 AN: 41484

American (AMR) AF: 0.102 AC: 1556 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 376 AN: 3466

East Asian (EAS) AF: 0.0179 AC: 93 AN: 5182

South Asian (SAS) AF: 0.117 AC: 565 AN: 4814

European-Finnish (FIN) AF: 0.126 AC: 1336 AN: 10608

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

European-Non Finnish (NFE) AF: 0.132 AC: 8966 AN: 68002

Other (OTH) AF: 0.150 AC: 317 AN: 2110

Alfa AF: 0.139 Hom.: 7166

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
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs16903097; hg19: chr8-129556356;