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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02045	XR_924565.1	n.86+2662G>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02045	ENST00000460324.3	n.408+2662G>T		intron_variant	Intron 2 of 3	3
LINC02032	ENST00000470219.2	n.147-8529C>A		intron_variant	Intron 2 of 2	3
LINC02032	ENST00000477153.1	n.272-8529C>A		intron_variant	Intron 2 of 2	3

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 v4.3

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;