rs9554166

Variant names:

• chr13-27823859-A-G
• rs9554166
• ENST00000499662.3:n.809-487T>C

Variant summary

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

The ENST00000499662.3(PLUT):​n.809-487T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 152,084 control chromosomes in the GnomAD database, including 6,747 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 0.29 (6747 hom., cov: 32)
• Consequence: PLUT ENST00000499662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLUT	NR_047484.2	n.802-1028T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLUT	ENST00000499662.3	n.809-487T>C		intron_variant	Intron 3 of 4	3

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43327 AN: 151966 Hom.: 6738 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.209

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.304

Gnomad EAS AF: 0.633

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.285 AC: 43362 AN: 152084 Hom.: 6747 Cov.: 32 AF XY: 0.293 AC XY: 21817 AN XY: 74350

African (AFR) AF: 0.307 AC: 12737 AN: 41476

American (AMR) AF: 0.333 AC: 5087 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.304 AC: 1053 AN: 3466

East Asian (EAS) AF: 0.633 AC: 3270 AN: 5168

South Asian (SAS) AF: 0.442 AC: 2128 AN: 4818

European-Finnish (FIN) AF: 0.285 AC: 3008 AN: 10568

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15228 AN: 67992

Other (OTH) AF: 0.279 AC: 588 AN: 2108

Alfa AF: 0.249 Hom.: 9350

Bravo AF: 0.288

Asia WGS AF: 0.512 AC: 1776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.74
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs9554166; hg19: chr13-28397996;