5-60491464-T-C

Position:

• chr5-60491464-T-C

Variant summary

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

The ENST00000515734.2(PART1):​n.2515T>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 0.441 in 151,956 control chromosomes in the GnomAD database, including 16,169 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 0.44 (16169 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: PART1 ENST00000515734.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.343

Genes affected

PART1 (HGNC:17263): (prostate androgen-regulated transcript 1) This gene is induced by androgen in prostate adenocarcinoma cells. Multiple alternatively transcript variants have been described for this gene, none of which are predicted to encode a protein product. [provided by RefSeq, Sep 2009]

PDE4D (HGNC:8783): (phosphodiesterase 4D) This gene encodes one of four mammalian counterparts to the fruit fly 'dunce' gene. The encoded protein has 3',5'-cyclic-AMP phosphodiesterase activity and degrades cAMP, which acts as a signal transduction molecule in multiple cell types. This gene uses different promoters to generate multiple alternatively spliced transcript variants that encode functional proteins.[provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Benign. Variant got -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 = 0.628 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PART1	NR_024617.1	n.711+3041T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PART1	ENST00000506884.2	n.300+3041T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.441 AC: 66951 AN: 151838 Hom.: 16116 Cov.: 31

Gnomad AFR AF: 0.634

Gnomad AMI AF: 0.276

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.563

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.273

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.407

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.441 AC: 67049 AN: 151956 Hom.: 16169 Cov.: 31 AF XY: 0.439 AC XY: 32571 AN XY: 74274

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.373

Gnomad4 ASJ AF: 0.341

Gnomad4 EAS AF: 0.563

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.273

Gnomad4 NFE AF: 0.353

Gnomad4 OTH AF: 0.414

Alfa AF: 0.387 Hom.: 2070

Bravo AF: 0.452

Asia WGS AF: 0.600 AC: 2082 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.9
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs153031; hg19: chr5-59787291;