chr13-65920232-T-A

Variant names:

• chr13-65920232-T-A
• rs9317546
• ENST00000665754.1:n.194-2021T>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01052	ENST00000665754.1	n.194-2021T>A		intron_variant	Intron 2 of 2

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;