rs10513332

Variant names:

• chr3-148150339-A-C
• rs10513332
• ENST00000733390.1:n.410+45390T>G

Your query was ambiguous. Multiple possible variants found:

• chr3-148150339-A-C
• chr3-148150339-A-T

Variant summary

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

The ENST00000733390.1(LINC02045):​n.410+45390T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.229 in 152,106 control chromosomes in the GnomAD database, including 4,497 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 0.23 (4497 hom., cov: 33)
• Consequence: LINC02045 ENST00000733390.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.484
• Publications: 1 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02045	ENST00000733390.1	n.410+45390T>G		intron_variant	Intron 2 of 4
LINC02032	ENST00000733533.1	n.306-10572A>C		intron_variant	Intron 3 of 5
LINC02032	ENST00000733534.1	n.111-10572A>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.229 AC: 34805 AN: 151988 Hom.: 4493 Cov.: 33

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.144

Gnomad EAS AF: 0.0762

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.216

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

GnomAD4 genome AF: 0.229 AC: 34829 AN: 152106 Hom.: 4497 Cov.: 33 AF XY: 0.227 AC XY: 16877 AN XY: 74354

African (AFR) AF: 0.342 AC: 14206 AN: 41490

American (AMR) AF: 0.200 AC: 3053 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.144 AC: 501 AN: 3470

East Asian (EAS) AF: 0.0763 AC: 396 AN: 5188

South Asian (SAS) AF: 0.136 AC: 656 AN: 4818

European-Finnish (FIN) AF: 0.225 AC: 2384 AN: 10584

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.191 AC: 13010 AN: 67974

Other (OTH) AF: 0.217 AC: 457 AN: 2110

Alfa AF: 0.197 Hom.: 4328

Bravo AF: 0.234

Asia WGS AF: 0.138 AC: 479 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.76
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs10513332; hg19: chr3-147868126;