rs456009

chr5-60500907-G-A

Variant summary

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

The NR_024617.1(PART1):n.711+12484G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.383 in 151,574 control chromosomes in the GnomAD database, including 11,311 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 0.38 (11311 hom., cov: 32)
• Consequence: PART1 NR_024617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.634

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PART1	NR_024617.1	n.711+12484G>A		intron_variant, non_coding_transcript_variant
PDE4D	XM_024446110.2	c.-90+21144C>T		intron_variant
PDE4D	XM_024446112.2	c.-90+21144C>T		intron_variant
PART1	NR_028509.1	n.492+12484G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PART1	ENST00000506884.2	n.300+12484G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.383 AC: 58011 AN: 151456 Hom.: 11292 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.449

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.416

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.406

Gnomad OTH AF: 0.384

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.383 AC: 58050 AN: 151574 Hom.: 11311 Cov.: 32 AF XY: 0.387 AC XY: 28660 AN XY: 74068

Gnomad4 AFR AF: 0.307

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.416

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.416

Gnomad4 NFE AF: 0.406

Gnomad4 OTH AF: 0.391

Alfa AF: 0.387 Hom.: 2584

Bravo AF: 0.379

Asia WGS AF: 0.480 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	4.9
Dann	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs456009; hg19: chr5-59796734;