chr13-27917249-T-C

Variant names:

• chr13-27917249-T-C
• rs2293942
• ENST00000499662.3:n.50A>G

Variant summary

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

The ENST00000499662.3(PLUT):​n.50A>G 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 0.191 in 152,230 control chromosomes in the GnomAD database, including 3,382 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 0.19 (3382 hom., cov: 32)
  • Exomes 𝑓: 0.25 (0 hom.)
• Consequence: PLUT ENST00000499662.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.12
• Publications: 3 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=-0.29).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PLUT	NR_047484.2	n.43A>G		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.50A>G		non_coding_transcript_exon_variant	Exon 1 of 5	3

Frequencies

GnomAD3 genomes AF: 0.191 AC: 29011 AN: 152108 Hom.: 3384 Cov.: 32

Gnomad AFR AF: 0.0524

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.283

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.220

GnomAD4 exome AF: 0.250 AC: 1 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 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) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.191 AC: 29008 AN: 152226 Hom.: 3382 Cov.: 32 AF XY: 0.192 AC XY: 14280 AN XY: 74416

African (AFR) AF: 0.0522 AC: 2172 AN: 41582

American (AMR) AF: 0.184 AC: 2819 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.221 AC: 768 AN: 3470

East Asian (EAS) AF: 0.268 AC: 1385 AN: 5166

South Asian (SAS) AF: 0.283 AC: 1367 AN: 4828

European-Finnish (FIN) AF: 0.220 AC: 2332 AN: 10588

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17379 AN: 67986

Other (OTH) AF: 0.222 AC: 470 AN: 2114

Alfa AF: 0.206 Hom.: 482

Bravo AF: 0.179

Asia WGS AF: 0.271 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	17
DANN	Benign	0.62
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs2293942; hg19: chr13-28491386;