rs187481

Variant names:

• chr5-60548019-C-G
• rs187481
• ENST00000506884.2:n.2446C>G

Variant summary

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

The ENST00000506884.2(PART1):​n.2446C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.734 in 152,136 control chromosomes in the GnomAD database, including 42,170 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 0.73 (42170 hom., cov: 31)
• Consequence: PART1 ENST00000506884.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 3 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000506884.2	n.2446C>G		non_coding_transcript_exon_variant	Exon 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.734 AC: 111515 AN: 152018 Hom.: 42108 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.651

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.660

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.734 AC: 111630 AN: 152136 Hom.: 42170 Cov.: 31 AF XY: 0.727 AC XY: 54067 AN XY: 74362

African (AFR) AF: 0.932 AC: 38709 AN: 41532

American (AMR) AF: 0.697 AC: 10653 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2457 AN: 3470

East Asian (EAS) AF: 0.651 AC: 3366 AN: 5174

South Asian (SAS) AF: 0.563 AC: 2706 AN: 4806

European-Finnish (FIN) AF: 0.623 AC: 6588 AN: 10578

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.660 AC: 44830 AN: 67964

Other (OTH) AF: 0.723 AC: 1528 AN: 2114

Alfa AF: 0.708 Hom.: 4849

Bravo AF: 0.748

Asia WGS AF: 0.672 AC: 2342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.53
DANN	Benign	0.47
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs187481; hg19: chr5-59843846;