5-60527291-C-T

Variant names:

• chr5-60527291-C-T
• rs26950
• ENST00000506884.2:n.301-2113C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000506884.2(PART1):​n.301-2113C>T variant causes a intron 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 ENST00000506884.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.246
• Publications: 7 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506884.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PART1	NR_024617.1		n.712-2113C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PART1	ENST00000506884.2	TSL:2	n.301-2113C>T		intron	N/A
	PART1	ENST00000663388.1		n.410-6641C>T		intron	N/A
	PART1	ENST00000664492.1		n.236-2113C>T		intron	N/A

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

African (AFR) AF: 0.0936 AC: 3881 AN: 41466

American (AMR) AF: 0.448 AC: 6841 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1419 AN: 3462

East Asian (EAS) AF: 0.552 AC: 2842 AN: 5148

South Asian (SAS) AF: 0.272 AC: 1310 AN: 4808

European-Finnish (FIN) AF: 0.390 AC: 4118 AN: 10564

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.395 AC: 26836 AN: 67950

Other (OTH) AF: 0.344 AC: 727 AN: 2112

Alfa AF: 0.356 Hom.: 10491

Bravo AF: 0.320

Asia WGS AF: 0.392 AC: 1365 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.52
DANN	Benign	0.61
PhyloP100		-0.25

Splicing

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

Other links and lift over

dbSNP: rs26950; hg19: chr5-59823118;