5-60527291-C-T

Position:

• chr5-60527291-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.712-2113C>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 0.319 in 151,996 control chromosomes in the GnomAD database, including 9,442 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 0.32 (9442 hom., cov: 32)
• Consequence: PART1 NR_024617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PART1	NR_024617.1	n.712-2113C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000506884.2	n.301-2113C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48527 AN: 151876 Hom.: 9442 Cov.: 32

Gnomad AFR AF: 0.0939

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.448

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.272

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.395

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.319 AC: 48514 AN: 151996 Hom.: 9442 Cov.: 32 AF XY: 0.322 AC XY: 23881 AN XY: 74248

Gnomad4 AFR AF: 0.0936

Gnomad4 AMR AF: 0.448

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.552

Gnomad4 SAS AF: 0.272

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.395

Gnomad4 OTH AF: 0.344

Alfa AF: 0.337 Hom.: 4569

Bravo AF: 0.320

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs26950; hg19: chr5-59823118;