rs599779

chr1-199369020-A-Cchr1-199369020-A-T

Variant summary

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

The NR_147896.1(LINC02789):n.310-22301A>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 0.623 in 151,744 control chromosomes in the GnomAD database, including 29,891 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 0.62 (29891 hom., cov: 31)
• Consequence: LINC02789 NR_147896.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24

Genes affected

LINC02789 (HGNC:54310): (long intergenic non-protein coding RNA 2789)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.726 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02789	NR_147896.1	n.310-22301A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02789	ENST00000452199.1	n.310-22301A>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94378 AN: 151626 Hom.: 29849 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.654

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.575

Gnomad OTH AF: 0.622

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

GnomAD4 genome AF: 0.623 AC: 94477 AN: 151744 Hom.: 29891 Cov.: 31 AF XY: 0.619 AC XY: 45850 AN XY: 74120

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.575

Gnomad4 OTH AF: 0.621

Alfa AF: 0.558 Hom.: 9516

Bravo AF: 0.641

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.0
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs599779; hg19: chr1-199338148;