chr13-27902841-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 12 publications found

Genes affected

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

LOC105370130 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

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.142+14309G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLUT	ENST00000499662.3	TSL:3	n.149+14309G>A		intron	N/A

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

African (AFR) AF: 0.201 AC: 8323 AN: 41358

American (AMR) AF: 0.300 AC: 4528 AN: 15078

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1188 AN: 3466

East Asian (EAS) AF: 0.400 AC: 2045 AN: 5118

South Asian (SAS) AF: 0.528 AC: 2535 AN: 4804

European-Finnish (FIN) AF: 0.399 AC: 4147 AN: 10398

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28378 AN: 67884

Other (OTH) AF: 0.356 AC: 746 AN: 2096

Alfa AF: 0.389 Hom.: 38033

Bravo AF: 0.325

Asia WGS AF: 0.451 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.0
DANN	Benign	0.71
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9554197; hg19: chr13-28476978;