rs1456669

Positions:

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

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000460324.2(LINC02045):​n.407+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 ENST00000460324.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.913

Genes affected

LINC02045 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LINC02045	XR_924565.1	n.86+2662G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC02045	ENST00000460324.2	n.407+2662G>T		intron_variant		3
ENSG00000244650	ENST00000470219.2	n.147-8529C>A		intron_variant		3
ENSG00000244650	ENST00000477153.1	n.272-8529C>A		intron_variant		3
LINC02045	ENST00000662134.1	n.420+2662G>T		intron_variant

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

Gnomad4 AFR AF: 0.0965

Gnomad4 AMR AF: 0.173

Gnomad4 ASJ AF: 0.119

Gnomad4 EAS AF: 0.219

Gnomad4 SAS AF: 0.188

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.122

Alfa AF: 0.137 Hom.: 726

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1456669; hg19: chr3-147935635;