13-27902841-C-T

Variant names:

• chr13-27902841-C-T
• rs9554197
• ENST00000499662.3:n.149+14309G>A

Variant summary

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

The ENST00000499662.3(PLUT):​n.149+14309G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,404 control chromosomes in the GnomAD database, including 9,762 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 0.35 (9762 hom., cov: 32)
• Consequence: PLUT ENST00000499662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.331

Genes affected

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

LOC105370130 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLUT	NR_047484.2	n.142+14309G>A		intron_variant	Intron 1 of 4
LOC105370130	XR_941788.2	n.159+68C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLUT	ENST00000499662.3	n.149+14309G>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52393 AN: 151298 Hom.: 9756 Cov.: 32

Gnomad AFR AF: 0.201

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.346 AC: 52416 AN: 151404 Hom.: 9762 Cov.: 32 AF XY: 0.350 AC XY: 25845 AN XY: 73918

Gnomad4 AFR AF: 0.201

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.343

Gnomad4 EAS AF: 0.400

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.356

Alfa AF: 0.405 Hom.: 26434

Bravo AF: 0.325

Asia WGS AF: 0.451 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9554197; hg19: chr13-28476978;