ENST00000506884.2:n.370T>C

Variant names:

• chr5-60529473-T-C
• rs26949
• ENST00000506884.2:n.370T>C

Variant summary

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

The ENST00000506884.2(PART1):​n.370T>C 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 0.349 in 152,150 control chromosomes in the GnomAD database, including 10,732 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 0.35 (10731 hom., cov: 33)
  • Exomes 𝑓: 0.67 (1 hom.)
• Consequence: PART1 ENST00000506884.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 14 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PART1	NR_024617.1	n.781T>C		non_coding_transcript_exon_variant	Exon 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000506884.2	n.370T>C		non_coding_transcript_exon_variant	Exon 2 of 4	2
PART1	ENST00000664492.1	n.305T>C		non_coding_transcript_exon_variant	Exon 2 of 3
PART1	ENST00000673670.1	n.963T>C		non_coding_transcript_exon_variant	Exon 3 of 5

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53079 AN: 152026 Hom.: 10730 Cov.: 33

Gnomad AFR AF: 0.139

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.445

Gnomad EAS AF: 0.554

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.373

GnomAD4 exome AF: 0.667 AC: 4 AN: 6 Hom.: 1 Cov.: 0 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.349 AC: 53065 AN: 152144 Hom.: 10731 Cov.: 33 AF XY: 0.352 AC XY: 26199 AN XY: 74380

African (AFR) AF: 0.139 AC: 5758 AN: 41524

American (AMR) AF: 0.462 AC: 7060 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.445 AC: 1544 AN: 3470

East Asian (EAS) AF: 0.554 AC: 2868 AN: 5174

South Asian (SAS) AF: 0.291 AC: 1400 AN: 4810

European-Finnish (FIN) AF: 0.447 AC: 4726 AN: 10580

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.418 AC: 28387 AN: 67976

Other (OTH) AF: 0.367 AC: 775 AN: 2110

Alfa AF: 0.402 Hom.: 25716

Bravo AF: 0.347

Asia WGS AF: 0.404 AC: 1409 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.35
DANN	Benign	0.51
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs26949; hg19: chr5-59825300;