rs9521585

chr13-110045914-G-T

Variant summary

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

The ENST00000670698.1(LINC03082):n.281-8943C>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.267 in 151,906 control chromosomes in the GnomAD database, including 6,528 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 0.27 (6528 hom., cov: 31)
• Consequence: LINC03082 ENST00000670698.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168

Genes affected

LINC03082 (HGNC:56676): (long intergenic non-protein coding RNA 3082)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC03082	XR_931725.4	n.305-8943C>A		intron_variant, non_coding_transcript_variant
LINC03082	XR_243070.4	n.195C>A		non_coding_transcript_exon_variant	1/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC03082	ENST00000670698.1	n.281-8943C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.268 AC: 40651 AN: 151788 Hom.: 6534 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.394

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.0690

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.267 AC: 40626 AN: 151906 Hom.: 6528 Cov.: 31 AF XY: 0.261 AC XY: 19368 AN XY: 74214

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.0693

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.283

Alfa AF: 0.346 Hom.: 12801

Bravo AF: 0.253

Asia WGS AF: 0.136 AC: 473 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.54
Dann	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9521585; hg19: chr13-110698261;