rs9317546

chr13-65920232-T-A

Variant summary

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

The ENST00000665754.1(LINC01052):n.194-2021T>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 0.303 in 152,020 control chromosomes in the GnomAD database, including 7,408 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 0.30 (7408 hom., cov: 32)
• Consequence: LINC01052 ENST00000665754.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103

Genes affected

LINC01052 (HGNC:49046): (long intergenic non-protein coding RNA 1052)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01052	ENST00000665754.1	n.194-2021T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.303 AC: 46039 AN: 151904 Hom.: 7399 Cov.: 32

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.317

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.268

Gnomad NFE AF: 0.358

Gnomad OTH AF: 0.292

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

GnomAD4 genome AF: 0.303 AC: 46061 AN: 152020 Hom.: 7408 Cov.: 32 AF XY: 0.304 AC XY: 22619 AN XY: 74294

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.317

Gnomad4 ASJ AF: 0.316

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.358

Gnomad4 OTH AF: 0.298

Alfa AF: 0.330 Hom.: 1032

Bravo AF: 0.295

Asia WGS AF: 0.343 AC: 1188 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	2.7
Dann	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9317546; hg19: chr13-66494364;