rs2293942

Positions:

• chr13-27917249-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_047484.2(PLUT):​n.43A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.191 in 152,230 control chromosomes in the GnomAD database, including 3,382 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 0.19 (3382 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: PLUT NR_047484.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLUT	NR_047484.2	n.43A>G		non_coding_transcript_exon_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLUT	ENST00000499662.3	n.50A>G		non_coding_transcript_exon_variant	1/5	3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29011 AN: 152108 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 FIN exome AF: 0.250

GnomAD4 genome AF: 0.191 AC: 29008 AN: 152226 Hom.: 3382 Cov.: 32 AF XY: 0.192 AC XY: 14280 AN XY: 74416

Gnomad4 AFR AF: 0.0522

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.283

Gnomad4 FIN AF: 0.220

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.222

Alfa AF: 0.211 Hom.: 481

Bravo AF: 0.179

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	17
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2293942; hg19: chr13-28491386;