rs1456669

Variant names:

• chr3-148217848-C-A
• rs1456669
• ENST00000460324.3:n.408+2662G>T

Your query was ambiguous. Multiple possible variants found:

• chr3-148217848-C-A
• chr3-148217848-C-G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000460324.3(LINC02045):​n.408+2662G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,812 control chromosomes in the GnomAD database, including 1,419 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 0.13 (1419 hom., cov: 32)
• Consequence: LINC02045 ENST00000460324.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913
• Publications: 8 publications found

Genes affected

LINC02045 (HGNC:52885): (long intergenic non-protein coding RNA 2045)

LINC02032 (HGNC:52866): (long intergenic non-protein coding RNA 2032)

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.208 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000460324.3. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02045	ENST00000460324.3	TSL:3	n.408+2662G>T		intron	N/A
	LINC02032	ENST00000470219.2	TSL:3	n.147-8529C>A		intron	N/A
	LINC02032	ENST00000477153.1	TSL:3	n.272-8529C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19874 AN: 151694 Hom.: 1413 Cov.: 32

Gnomad AFR AF: 0.0962

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.172

Gnomad ASJ AF: 0.119

Gnomad EAS AF: 0.219

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.131 AC: 19902 AN: 151812 Hom.: 1419 Cov.: 32 AF XY: 0.135 AC XY: 10024 AN XY: 74200

African (AFR) AF: 0.0965 AC: 4000 AN: 41452

American (AMR) AF: 0.173 AC: 2622 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.119 AC: 412 AN: 3468

East Asian (EAS) AF: 0.219 AC: 1124 AN: 5134

South Asian (SAS) AF: 0.188 AC: 903 AN: 4810

European-Finnish (FIN) AF: 0.158 AC: 1669 AN: 10558

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.129 AC: 8785 AN: 67890

Other (OTH) AF: 0.122 AC: 257 AN: 2098

Alfa AF: 0.132 Hom.: 2334

Bravo AF: 0.130

Asia WGS AF: 0.181 AC: 628 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	18
DANN	Benign	0.52
PhyloP100		0.91
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1456669; hg19: chr3-147935635;