rs9512900

chr13-27855601-T-C

Variant summary

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

The NR_047484.2(PLUT):n.143-7065A>G 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 0.239 in 152,126 control chromosomes in the GnomAD database, including 5,532 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 0.24 (5532 hom., cov: 32)
• Consequence: PLUT NR_047484.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.351 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLUT	NR_047484.2	n.143-7065A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLUT	ENST00000499662.3	n.150-7065A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36391 AN: 152008 Hom.: 5530 Cov.: 32

Gnomad AFR AF: 0.0810

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.226

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.0210

Gnomad SAS AF: 0.183

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.405

Gnomad NFE AF: 0.355

Gnomad OTH AF: 0.289

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

GnomAD4 genome AF: 0.239 AC: 36381 AN: 152126 Hom.: 5532 Cov.: 32 AF XY: 0.231 AC XY: 17175 AN XY: 74378

Gnomad4 AFR AF: 0.0808

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.0210

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.285

Alfa AF: 0.319 Hom.: 2855

Bravo AF: 0.233

Asia WGS AF: 0.0900 AC: 312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.2
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9512900; hg19: chr13-28429738;