13-27906219-C-T

Variant names:

• chr13-27906219-C-T
• rs9551419
• ENST00000499662.3:n.149+10931G>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+10931G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 152,142 control chromosomes in the GnomAD database, including 1,866 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 0.15 (1866 hom., cov: 32)
• Consequence: PLUT ENST00000499662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.585
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLUT	NR_047484.2	n.142+10931G>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLUT	ENST00000499662.3	n.149+10931G>A		intron_variant	Intron 1 of 4	3

Frequencies

GnomAD3 genomes AF: 0.154 AC: 23436 AN: 152024 Hom.: 1866 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.256

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.132

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

GnomAD4 genome AF: 0.154 AC: 23459 AN: 152142 Hom.: 1866 Cov.: 32 AF XY: 0.156 AC XY: 11637 AN XY: 74382

African (AFR) AF: 0.150 AC: 6249 AN: 41530

American (AMR) AF: 0.108 AC: 1648 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 358 AN: 3466

East Asian (EAS) AF: 0.154 AC: 793 AN: 5158

South Asian (SAS) AF: 0.256 AC: 1233 AN: 4816

European-Finnish (FIN) AF: 0.173 AC: 1831 AN: 10582

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10864 AN: 67982

Other (OTH) AF: 0.131 AC: 276 AN: 2112

Alfa AF: 0.149 Hom.: 327

Bravo AF: 0.146

Asia WGS AF: 0.192 AC: 667 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.71
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs9551419; hg19: chr13-28480356;