3-46417451-G-A

Position:

• chr3-46417451-G-A

Variant summary

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

The NR_151704.1(LINC02009):​n.2100C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.185 in 152,042 control chromosomes in the GnomAD database, including 3,313 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 0.18 (3313 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: LINC02009 NR_151704.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575

Genes affected

LINC02009 (HGNC:52845): (long intergenic non-protein coding RNA 2009)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC02009	NR_151704.1	n.2100C>T		non_coding_transcript_exon_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC02009	ENST00000635852.1	n.2024C>T		non_coding_transcript_exon_variant	5/5	3
LINC02009	ENST00000661642.1	n.1890C>T		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28036 AN: 151922 Hom.: 3307 Cov.: 32

Gnomad AFR AF: 0.333

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.105

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.152

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.139

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.185 AC: 28079 AN: 152040 Hom.: 3313 Cov.: 32 AF XY: 0.179 AC XY: 13271 AN XY: 74312

Gnomad4 AFR AF: 0.333

Gnomad4 AMR AF: 0.105

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0218

Gnomad4 FIN AF: 0.152

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.138

Alfa AF: 0.173 Hom.: 364

Bravo AF: 0.189

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6791599; hg19: chr3-46458942;