13-27917061-G-A

Variant names:

• chr13-27917061-G-A
• rs2293941
• ENST00000499662.3:n.149+89C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000499662.3(PLUT):​n.149+89C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.228 in 151,930 control chromosomes in the GnomAD database, including 4,343 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 0.23 (4343 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: PLUT ENST00000499662.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.897
• Publications: 40 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000499662.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLUT	NR_047484.2		n.142+89C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PLUT	ENST00000499662.3	TSL:3	n.149+89C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34686 AN: 151808 Hom.: 4334 Cov.: 32

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.182

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.204

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.251

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

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: 0.228 AC: 34712 AN: 151928 Hom.: 4343 Cov.: 32 AF XY: 0.234 AC XY: 17372 AN XY: 74252

African (AFR) AF: 0.167 AC: 6926 AN: 41422

American (AMR) AF: 0.339 AC: 5166 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.313 AC: 1085 AN: 3472

East Asian (EAS) AF: 0.454 AC: 2348 AN: 5176

South Asian (SAS) AF: 0.175 AC: 842 AN: 4800

European-Finnish (FIN) AF: 0.253 AC: 2665 AN: 10544

Middle Eastern (MID) AF: 0.199 AC: 58 AN: 292

European-Non Finnish (NFE) AF: 0.220 AC: 14931 AN: 67962

Other (OTH) AF: 0.250 AC: 526 AN: 2106

Alfa AF: 0.226 Hom.: 17994

Bravo AF: 0.234

Asia WGS AF: 0.278 AC: 966 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.9
DANN	Benign	0.65
PhyloP100		0.90

Splicing

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

Other links and lift over

dbSNP: rs2293941; hg19: chr13-28491198;