rs9317546

Variant names:

• chr13-65920232-T-A
• rs9317546
• ENST00000665754.1:n.194-2021T>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 0 publications found

Genes affected

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

ENSG00000300318 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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
ENSG00000300318	ENST00000770902.1	n.234+30461A>T		intron_variant	Intron 2 of 2
LINC01052	ENST00000771091.1	n.194-9176T>A		intron_variant	Intron 2 of 6

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

African (AFR) AF: 0.194 AC: 8045 AN: 41492

American (AMR) AF: 0.317 AC: 4836 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1098 AN: 3472

East Asian (EAS) AF: 0.272 AC: 1405 AN: 5162

South Asian (SAS) AF: 0.351 AC: 1690 AN: 4818

European-Finnish (FIN) AF: 0.344 AC: 3634 AN: 10558

Middle Eastern (MID) AF: 0.267 AC: 78 AN: 292

European-Non Finnish (NFE) AF: 0.358 AC: 24291 AN: 67936

Other (OTH) AF: 0.298 AC: 630 AN: 2114

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
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs9317546; hg19: chr13-66494364;