rs2293941

Positions:

• chr13-27917061-G-A
• chr13-27917061-G-C
• chr13-27917061-G-T

Variant summary

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

The NR_047484.2(PLUT):​n.142+89C>T variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,930 control chromosomes in the GnomAD database, including 4,343 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 0.23 (4343 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PLUT NR_047484.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLUT	NR_047484.2	n.142+89C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLUT	ENST00000499662.3	n.149+89C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34686 AN: 151808 Hom.: 4334 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.251

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AC XY: 0 AN XY: 0

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.228 AC: 34712 AN: 151928 Hom.: 4343 Cov.: 32 AF XY: 0.234 AC XY: 17372 AN XY: 74252

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.339

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.175

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.220

Gnomad4 OTH AF: 0.250

Alfa AF: 0.226 Hom.: 7992

Bravo AF: 0.234

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2293941; hg19: chr13-28491198;