rs9290705

Variant names:

• chr3-180456679-T-C
• rs9290705
• ENST00000654328.1:n.265-18760T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654328.1(LINC02053):​n.265-18760T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 152,150 control chromosomes in the GnomAD database, including 687 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 0.091 (687 hom., cov: 32)
• Consequence: LINC02053 ENST00000654328.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.293

Genes affected

LINC02053 (HGNC:52893): (long intergenic non-protein coding RNA 2053)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.114 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
LINC02053	ENST00000654328.1	n.265-18760T>C		intron_variant	Intron 1 of 1
LINC02053	ENST00000668671.1	n.283-2964T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0911 AC: 13846 AN: 152032 Hom.: 686 Cov.: 32

Gnomad AFR AF: 0.0706

Gnomad AMI AF: 0.0757

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.0960

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0785

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0995

Gnomad OTH AF: 0.0912

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

GnomAD4 genome AF: 0.0910 AC: 13850 AN: 152150 Hom.: 687 Cov.: 32 AF XY: 0.0927 AC XY: 6891 AN XY: 74372

Gnomad4 AFR AF: 0.0704

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.0960

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0792

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.0995

Gnomad4 OTH AF: 0.0903

Alfa AF: 0.0981 Hom.: 1025

Bravo AF: 0.0898

Asia WGS AF: 0.0420 AC: 146 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.052
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290705; hg19: chr3-180174467;