rs10516153

chr5-60524034-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.712-5370C>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 0.0855 in 152,372 control chromosomes in the GnomAD database, including 1,611 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 0.086 (1611 hom., cov: 32)
  • Exomes 𝑓: 0.024 (0 hom.)
• Consequence: PART1 NR_024617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PART1	NR_024617.1	n.712-5370C>T		intron_variant, non_coding_transcript_variant
PART1	NR_028509.1	n.3507C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PART1	ENST00000506884.2	n.301-5370C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0854 AC: 12982 AN: 152090 Hom.: 1597 Cov.: 32

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00212

Gnomad SAS AF: 0.0437

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0664

GnomAD4 exome AF: 0.0244 AC: 4 AN: 164 Hom.: 0 Cov.: 0 AF XY: 0.0400 AC XY: 4 AN XY: 100

Gnomad4 AFR exome AF: 0.500

Gnomad4 ASJ exome AF: 0.500

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0278

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0856 AC: 13031 AN: 152208 Hom.: 1611 Cov.: 32 AF XY: 0.0828 AC XY: 6167 AN XY: 74438

Gnomad4 AFR AF: 0.273

Gnomad4 AMR AF: 0.0336

Gnomad4 ASJ AF: 0.0118

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.0437

Gnomad4 FIN AF: 0.00348

Gnomad4 NFE AF: 0.0105

Gnomad4 OTH AF: 0.0662

Alfa AF: 0.0378 Hom.: 218

Bravo AF: 0.0954

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.9
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10516153; hg19: chr5-59819861;