3-46417451-G-A

Variant names:

• chr3-46417451-G-A
• rs6791599
• ENST00000635852.1:n.2024C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000635852.1(LINC02009):​n.2024C>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 ENST00000635852.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.575
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000635852.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02009	NR_151704.1		n.2100C>T		non_coding_transcript_exon	Exon 5 of 5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02009	ENST00000635852.1	TSL:3	n.2024C>T		non_coding_transcript_exon	Exon 5 of 5
	LINC02009	ENST00000661642.1		n.1890C>T		non_coding_transcript_exon	Exon 4 of 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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.333 AC: 13794 AN: 41428

American (AMR) AF: 0.105 AC: 1603 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.151 AC: 523 AN: 3470

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5180

South Asian (SAS) AF: 0.0218 AC: 105 AN: 4812

European-Finnish (FIN) AF: 0.152 AC: 1610 AN: 10580

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9954 AN: 67968

Other (OTH) AF: 0.138 AC: 291 AN: 2114

Alfa AF: 0.226 Hom.: 1075

Bravo AF: 0.189

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.9
DANN	Benign	0.51
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs6791599; hg19: chr3-46458942;