rs9793739

chr1-229150111-G-A

Variant summary

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

The ENST00000666388.1(LINC02814):n.337+47587C>T 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 0.0973 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 ENST00000666388.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.523

Genes affected

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

LINC02815 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LINC02815	XR_002958488.1	n.415+33939C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02814	ENST00000666388.1	n.337+47587C>T		intron_variant, non_coding_transcript_variant
LINC02814	ENST00000662083.1	n.46+33939C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.140

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.135

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.0411

Gnomad4 NFE AF: 0.0612

Gnomad4 OTH AF: 0.0895

Alfa AF: 0.0721 Hom.: 454

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9793739; hg19: chr1-229285858;