13-27840128-A-G

Variant summary

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

The NR_047484.2(PLUT):n.672-5978T>C 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 0.205 in 152,156 control chromosomes in the GnomAD database, including 3,800 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 0.20 (3800 hom., cov: 33)
• Consequence: PLUT NR_047484.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.48

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLUT	NR_047484.2	n.672-5978T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLUT	ENST00000499662.3	n.679-5978T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31170 AN: 152038 Hom.: 3799 Cov.: 33

Gnomad AFR AF: 0.0799

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.223

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.205 AC: 31176 AN: 152156 Hom.: 3800 Cov.: 33 AF XY: 0.204 AC XY: 15202 AN XY: 74392

Gnomad4 AFR AF: 0.0798

Gnomad4 AMR AF: 0.194

Gnomad4 ASJ AF: 0.220

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.223

Gnomad4 FIN AF: 0.244

Gnomad4 NFE AF: 0.269

Gnomad4 OTH AF: 0.204

Alfa AF: 0.212 Hom.: 1569

Bravo AF: 0.197

Asia WGS AF: 0.230 AC: 797 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.040
Dann	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9551404; hg19: chr13-28414265;