chr8-46867313-C-A

Variant names:

• chr8-46867313-C-A
• rs7826304
• ENST00000659403.1:n.364+16570C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000659403.1(LINC00293):​n.364+16570C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.732 in 152,022 control chromosomes in the GnomAD database, including 40,865 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 0.73 (40865 hom., cov: 31)
• Consequence: LINC00293 ENST00000659403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.560
• Publications: 4 publications found

Genes affected

LINC00293 (HGNC:39078): (long intergenic non-protein coding RNA 293)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000659403.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00293	ENST00000659403.1		n.364+16570C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.732 AC: 111160 AN: 151904 Hom.: 40825 Cov.: 31

Gnomad AFR AF: 0.733

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.802

Gnomad ASJ AF: 0.703

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.659

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.740

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

GnomAD4 genome AF: 0.732 AC: 111258 AN: 152022 Hom.: 40865 Cov.: 31 AF XY: 0.728 AC XY: 54084 AN XY: 74284

African (AFR) AF: 0.734 AC: 30437 AN: 41482

American (AMR) AF: 0.802 AC: 12260 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.703 AC: 2438 AN: 3468

East Asian (EAS) AF: 0.857 AC: 4418 AN: 5158

South Asian (SAS) AF: 0.586 AC: 2817 AN: 4810

European-Finnish (FIN) AF: 0.659 AC: 6950 AN: 10554

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.729 AC: 49550 AN: 67954

Other (OTH) AF: 0.738 AC: 1557 AN: 2110

Alfa AF: 0.668 Hom.: 3065

Bravo AF: 0.747

Asia WGS AF: 0.722 AC: 2512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.0
DANN	Benign	0.22
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs7826304; hg19: chr8-47778935;