rs40512

chr5-60509640-C-T

Variant summary

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

The NR_024617.1(PART1):n.712-19764C>T 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 0.659 in 151,942 control chromosomes in the GnomAD database, including 34,464 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 0.66 (34464 hom., cov: 30)
• Consequence: PART1 NR_024617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.282

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.857 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PART1	NR_024617.1	n.712-19764C>T		intron_variant, non_coding_transcript_variant
PDE4D	XM_024446110.2	c.-90+12411G>A		intron_variant
PDE4D	XM_024446112.2	c.-90+12411G>A		intron_variant
PART1	NR_028509.1	n.493-11380C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PART1	ENST00000506884.2	n.301-19764C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100047 AN: 151822 Hom.: 34406 Cov.: 30

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.500

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.439

Gnomad SAS AF: 0.730

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.631

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

GnomAD4 genome AF: 0.659 AC: 100166 AN: 151942 Hom.: 34464 Cov.: 30 AF XY: 0.656 AC XY: 48683 AN XY: 74256

Gnomad4 AFR AF: 0.865

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.587

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.536

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.637

Alfa AF: 0.602 Hom.: 38502

Bravo AF: 0.666

Asia WGS AF: 0.597 AC: 2075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.5
Dann	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs40512; hg19: chr5-59805467;