rs2387100

Positions:

• chr13-27852622-A-G
• chr13-27852622-A-T

Variant summary

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

The NR_047484.2(PLUT):​n.143-4086T>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 0.271 in 152,026 control chromosomes in the GnomAD database, including 5,704 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 0.27 (5704 hom., cov: 31)
• Consequence: PLUT NR_047484.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.306 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PLUT	NR_047484.2	n.143-4086T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PLUT	ENST00000499662.3	n.150-4086T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.271 AC: 41177 AN: 151908 Hom.: 5689 Cov.: 31

Gnomad AFR AF: 0.271

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.318

Gnomad SAS AF: 0.302

Gnomad FIN AF: 0.246

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.274

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.271 AC: 41221 AN: 152026 Hom.: 5704 Cov.: 31 AF XY: 0.269 AC XY: 19993 AN XY: 74296

Gnomad4 AFR AF: 0.271

Gnomad4 AMR AF: 0.267

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.319

Gnomad4 SAS AF: 0.302

Gnomad4 FIN AF: 0.246

Gnomad4 NFE AF: 0.274

Gnomad4 OTH AF: 0.264

Alfa AF: 0.273 Hom.: 11700

Bravo AF: 0.276

Asia WGS AF: 0.314 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0040
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2387100; hg19: chr13-28426759;