rs9793739

Variant names:

• chr1-229150111-G-A
• rs9793739
• ENST00000662083.1:n.46+33939C>T

Variant summary

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

The ENST00000662083.1(LINC02814):​n.46+33939C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0973 in 152,226 control chromosomes in the GnomAD database, including 855 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 0.097 (855 hom., cov: 32)
• Consequence: LINC02814 ENST00000662083.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523
• Publications: 2 publications found

Genes affected

LINC02814 (HGNC:54346): (long intergenic non-protein coding RNA 2814)

LINC02815 (HGNC:54347): (long intergenic non-protein coding RNA 2815)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02815	NR_186725.1	n.156+4459C>T		intron_variant	Intron 1 of 3
LINC02815	NR_186726.1	n.156+4459C>T		intron_variant	Intron 1 of 2
LINC02815	NR_186727.1	n.156+4459C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02814	ENST00000662083.1	n.46+33939C>T		intron_variant	Intron 1 of 4
LINC02814	ENST00000666388.1	n.337+47587C>T		intron_variant	Intron 2 of 2
LINC02814	ENST00000716797.1	n.183+33939C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0972 AC: 14791 AN: 152108 Hom.: 852 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.121

Gnomad ASJ AF: 0.135

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0612

Gnomad OTH AF: 0.0914

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

GnomAD4 genome AF: 0.0973 AC: 14811 AN: 152226 Hom.: 855 Cov.: 32 AF XY: 0.0979 AC XY: 7289 AN XY: 74430

African (AFR) AF: 0.140 AC: 5794 AN: 41494

American (AMR) AF: 0.122 AC: 1859 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.135 AC: 468 AN: 3470

East Asian (EAS) AF: 0.179 AC: 926 AN: 5178

South Asian (SAS) AF: 0.173 AC: 835 AN: 4824

European-Finnish (FIN) AF: 0.0411 AC: 437 AN: 10620

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0612 AC: 4161 AN: 68036

Other (OTH) AF: 0.0895 AC: 189 AN: 2112

Alfa AF: 0.0762 Hom.: 1357

Bravo AF: 0.105

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.28
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs9793739; hg19: chr1-229285858;