rs9512900

Variant names:

• chr13-27855601-T-C
• rs9512900
• ENST00000499662.3:n.150-7065A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000499662.3(PLUT):​n.150-7065A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 152,126 control chromosomes in the GnomAD database, including 5,532 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 0.24 (5532 hom., cov: 32)
• Consequence: PLUT ENST00000499662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 9 publications found

Genes affected

PLUT (HGNC:43698): (PDX1 associated lncRNA, upregulator of transcription)

ACMG classification

Our verdict: Benign. The variant received -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 = 0.351 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499662.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLUT	NR_047484.2		n.143-7065A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLUT	ENST00000499662.3	TSL:3	n.150-7065A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36391 AN: 152008 Hom.: 5530 Cov.: 32

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.239 AC: 36381 AN: 152126 Hom.: 5532 Cov.: 32 AF XY: 0.231 AC XY: 17175 AN XY: 74378

African (AFR) AF: 0.0808 AC: 3353 AN: 41516

American (AMR) AF: 0.226 AC: 3452 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.344 AC: 1192 AN: 3466

East Asian (EAS) AF: 0.0210 AC: 109 AN: 5184

South Asian (SAS) AF: 0.183 AC: 882 AN: 4812

European-Finnish (FIN) AF: 0.211 AC: 2238 AN: 10582

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24125 AN: 67962

Other (OTH) AF: 0.285 AC: 601 AN: 2108

Alfa AF: 0.302 Hom.: 14284

Bravo AF: 0.233

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.2
DANN	Benign	0.71
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs9512900; hg19: chr13-28429738;