chr5-60522792-C-T

Variant names:

• chr5-60522792-C-T
• rs3857233
• ENST00000504876.2:n.1990C>T

Variant summary

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

The ENST00000504876.2(PART1):​n.1990C>T 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 0.0856 in 152,578 control chromosomes in the GnomAD database, including 1,610 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 (1610 hom., cov: 33)
  • Exomes 𝑓: 0.016 (0 hom.)
• Consequence: PART1 ENST00000504876.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152
• Publications: 2 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=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000504876.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PART1	NR_028509.1		n.2265C>T		non_coding_transcript_exon	Exon 2 of 2
	PART1	NR_024617.1		n.712-6612C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PART1	ENST00000504876.2	TSL:2	n.1990C>T		non_coding_transcript_exon	Exon 2 of 2
	PART1	ENST00000661844.1		n.2404C>T		non_coding_transcript_exon	Exon 2 of 2
	PART1	ENST00000673825.1		n.2034C>T		non_coding_transcript_exon	Exon 2 of 5

Frequencies

GnomAD3 genomes AF: 0.0855 AC: 13005 AN: 152146 Hom.: 1596 Cov.: 33

Gnomad AFR AF: 0.273

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0118

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.0439

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0105

Gnomad OTH AF: 0.0657

GnomAD4 exome AF: 0.0159 AC: 5 AN: 314 Hom.: 0 Cov.: 0 AF XY: 0.0129 AC XY: 3 AN XY: 232

African (AFR) AF: 0.167 AC: 2 AN: 12

American (AMR) AF: 0.00 AC: 0 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.00 AC: 0 AN: 12

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 32

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.00901 AC: 2 AN: 222

Other (OTH) AF: 0.0455 AC: 1 AN: 22

GnomAD4 genome AF: 0.0857 AC: 13054 AN: 152264 Hom.: 1610 Cov.: 33 AF XY: 0.0830 AC XY: 6181 AN XY: 74462

African (AFR) AF: 0.274 AC: 11361 AN: 41516

American (AMR) AF: 0.0337 AC: 515 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0118 AC: 41 AN: 3470

East Asian (EAS) AF: 0.00212 AC: 11 AN: 5190

South Asian (SAS) AF: 0.0439 AC: 212 AN: 4828

European-Finnish (FIN) AF: 0.00348 AC: 37 AN: 10622

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0105 AC: 713 AN: 68024

Other (OTH) AF: 0.0655 AC: 138 AN: 2108

Alfa AF: 0.0674 Hom.: 184

Bravo AF: 0.0955

Asia WGS AF: 0.0400 AC: 138 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.33
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs3857233; hg19: chr5-59818619;