ENST00000615939.1:n.152T>C

Variant names:

• chr19-17510699-A-G
• rs1078000
• ENST00000615939.1:n.152T>C

Variant summary

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

The ENST00000615939.1(PGLS-DT):​n.152T>C 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 0.611 in 152,036 control chromosomes in the GnomAD database, including 29,331 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 0.61 (29325 hom., cov: 32)
  • Exomes 𝑓: 0.67 (6 hom.)
• Consequence: PGLS-DT ENST00000615939.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 5 publications found

Genes affected

PGLS-DT (HGNC:55274): (PGLS divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000615939.1. 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
	PGLS-DT	NR_147835.1		n.547+644T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PGLS-DT	ENST00000615939.1	TSL:6	n.152T>C		non_coding_transcript_exon	Exon 1 of 1
	PGLS-DT	ENST00000595116.3	TSL:3	n.220+644T>C		intron	N/A
	PGLS-DT	ENST00000596643.5	TSL:3	n.547+644T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.610 AC: 92697 AN: 151894 Hom.: 29264 Cov.: 32

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.457

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.535

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.470

Gnomad FIN AF: 0.596

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.526

Gnomad OTH AF: 0.625

GnomAD4 exome AF: 0.667 AC: 16 AN: 24 Hom.: 6 Cov.: 0 AF XY: 0.611 AC XY: 11 AN XY: 18

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.00 AC: 0 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 9 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.875 AC: 7 AN: 8

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.611 AC: 92814 AN: 152012 Hom.: 29325 Cov.: 32 AF XY: 0.615 AC XY: 45668 AN XY: 74314

African (AFR) AF: 0.783 AC: 32500 AN: 41484

American (AMR) AF: 0.639 AC: 9746 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.535 AC: 1855 AN: 3468

East Asian (EAS) AF: 0.483 AC: 2486 AN: 5150

South Asian (SAS) AF: 0.470 AC: 2266 AN: 4826

European-Finnish (FIN) AF: 0.596 AC: 6288 AN: 10550

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.526 AC: 35750 AN: 67964

Other (OTH) AF: 0.626 AC: 1320 AN: 2110

Alfa AF: 0.550 Hom.: 99325

Bravo AF: 0.624

Asia WGS AF: 0.512 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.71
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1078000; hg19: chr19-17621508;