rs4133470

Positions:

• chr5-60522419-T-C

Variant summary

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

The NR_024617.1(PART1):​n.712-6985T>C 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 0.385 in 152,064 control chromosomes in the GnomAD database, including 15,576 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 (15575 hom., cov: 32)
  • Exomes 𝑓: 0.29 (1 hom.)
• Consequence: PART1 NR_024617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PART1	NR_024617.1	n.712-6985T>C		intron_variant, non_coding_transcript_variant
PART1	NR_028509.1	n.1892T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000506884.2	n.301-6985T>C		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58373 AN: 151932 Hom.: 15519 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.286 AC: 4 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.400 AC XY: 4 AN XY: 10

Gnomad4 AFR exome AF: 1.00

Gnomad4 NFE exome AF: 0.167

GnomAD4 genome AF: 0.385 AC: 58482 AN: 152050 Hom.: 15575 Cov.: 32 AF XY: 0.376 AC XY: 27969 AN XY: 74306

Gnomad4 AFR AF: 0.761

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.0419

Gnomad4 SAS AF: 0.204

Gnomad4 FIN AF: 0.248

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.349

Alfa AF: 0.272 Hom.: 10325

Bravo AF: 0.399

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.0
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4133470; hg19: chr5-59818246; COSMIC: COSV72259938;