rs26956

chr5-60495158-C-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+6735C>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 0.231 in 152,154 control chromosomes in the GnomAD database, including 4,953 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 (4953 hom., cov: 32)
• Consequence: PART1 NR_024617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

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=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PART1	NR_024617.1	n.711+6735C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PART1	ENST00000506884.2	n.300+6735C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35203 AN: 152036 Hom.: 4941 Cov.: 32

Gnomad AFR AF: 0.0744

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.389

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.288

Gnomad OTH AF: 0.235

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

GnomAD4 genome AF: 0.231 AC: 35218 AN: 152154 Hom.: 4953 Cov.: 32 AF XY: 0.236 AC XY: 17590 AN XY: 74394

Gnomad4 AFR AF: 0.0742

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.288

Gnomad4 OTH AF: 0.244

Alfa AF: 0.274 Hom.: 8216

Bravo AF: 0.222

Asia WGS AF: 0.410 AC: 1422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	6.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs26956; hg19: chr5-59790985;