rs2293943

Variant names:

• chr13-27917262-A-T
• rs2293943
• ENST00000499662.3:n.37T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000499662.3(PLUT):​n.37T>A 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 0.557 in 152,060 control chromosomes in the GnomAD database, including 25,482 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 0.56 (25482 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PLUT ENST00000499662.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.806 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLUT	NR_047484.2	n.30T>A		non_coding_transcript_exon_variant	Exon 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PLUT	ENST00000499662.3	n.37T>A		non_coding_transcript_exon_variant	Exon 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.558 AC: 84722 AN: 151940 Hom.: 25469 Cov.: 33

Gnomad AFR AF: 0.314

Gnomad AMI AF: 0.638

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.656

Gnomad EAS AF: 0.826

Gnomad SAS AF: 0.699

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.639

Gnomad OTH AF: 0.594

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.557 AC: 84769 AN: 152058 Hom.: 25482 Cov.: 33 AF XY: 0.566 AC XY: 42043 AN XY: 74306

African (AFR) AF: 0.315 AC: 13053 AN: 41494

American (AMR) AF: 0.623 AC: 9523 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.656 AC: 2276 AN: 3468

East Asian (EAS) AF: 0.826 AC: 4267 AN: 5164

South Asian (SAS) AF: 0.699 AC: 3363 AN: 4814

European-Finnish (FIN) AF: 0.651 AC: 6863 AN: 10546

Middle Eastern (MID) AF: 0.575 AC: 169 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43412 AN: 67964

Other (OTH) AF: 0.597 AC: 1261 AN: 2114

Alfa AF: 0.586 Hom.: 3398

Bravo AF: 0.541

Asia WGS AF: 0.706 AC: 2452 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	15
DANN	Benign	0.85
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2293943; hg19: chr13-28491399;