rs1898240

Positions:

• chr1-199377952-A-G

Variant summary

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

The NR_147896.1(LINC02789):​n.310-13369A>G 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 0.202 in 151,848 control chromosomes in the GnomAD database, including 3,252 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 0.20 (3252 hom., cov: 32)
• Consequence: LINC02789 NR_147896.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.43

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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.321 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC02789	NR_147896.1	n.310-13369A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02789	ENST00000452199.1	n.310-13369A>G		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30723 AN: 151728 Hom.: 3255 Cov.: 32

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.171

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.336

Gnomad SAS AF: 0.166

Gnomad FIN AF: 0.242

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.216

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.202 AC: 30720 AN: 151848 Hom.: 3252 Cov.: 32 AF XY: 0.203 AC XY: 15082 AN XY: 74198

Gnomad4 AFR AF: 0.171

Gnomad4 AMR AF: 0.171

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.335

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.242

Gnomad4 NFE AF: 0.216

Gnomad4 OTH AF: 0.194

Alfa AF: 0.211 Hom.: 6866

Bravo AF: 0.197

Asia WGS AF: 0.250 AC: 867 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.23
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1898240; hg19: chr1-199347080;