rs10494786

chr1-199226764-T-C

Variant summary

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

The NR_147896.1(LINC02789):n.309+64194T>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 0.147 in 152,042 control chromosomes in the GnomAD database, including 2,059 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 0.15 (2059 hom., cov: 32)
• Consequence: LINC02789 NR_147896.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.568

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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02789	NR_147896.1	n.309+64194T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02789	ENST00000452199.1	n.309+64194T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22406 AN: 151922 Hom.: 2059 Cov.: 32

Gnomad AFR AF: 0.0413

Gnomad AMI AF: 0.205

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.212

Gnomad SAS AF: 0.0775

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.195

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

GnomAD4 genome AF: 0.147 AC: 22410 AN: 152042 Hom.: 2059 Cov.: 32 AF XY: 0.145 AC XY: 10753 AN XY: 74338

Gnomad4 AFR AF: 0.0413

Gnomad4 AMR AF: 0.180

Gnomad4 ASJ AF: 0.188

Gnomad4 EAS AF: 0.213

Gnomad4 SAS AF: 0.0777

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.204

Gnomad4 OTH AF: 0.194

Alfa AF: 0.187 Hom.: 1548

Bravo AF: 0.149

Asia WGS AF: 0.140 AC: 488 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.20
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494786; hg19: chr1-199195892;