Genetic Variant PART1:n.3232C>T (chr5-60524034-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000504876.2(PART1):n.3232C>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 0.0855 in 152,372 control chromosomes in the GnomAD database, including 1,611 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 ( 1611 hom., cov: 32)

Exomes 𝑓: 0.024 ( 0 hom. )

Consequence

PART1
ENST00000504876.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.109

Publications

2 publications found

Variant links:

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]

PART1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PART1	NR_028509.1 link	n.3507C>T		non_coding_transcript_exon_variant	Exon 2 of 2
PART1	NR_024617.1 link	n.712-5370C>T		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PART1	ENST00000504876.2 link	n.3232C>T	non_coding_transcript_exon_variant	Exon 2 of 2	2
PART1	ENST00000661844.1 link	n.3646C>T	non_coding_transcript_exon_variant	Exon 2 of 2
PART1	ENST00000506884.2 link	n.301-5370C>T	intron_variant	Intron 1 of 3	2

Frequencies

GnomAD3 genomes

AF:

0.0854

AC:

12982

AN:

152090

Hom.:

1597

Cov.:

show subpopulations

Gnomad AFR

AF:

0.273

Gnomad AMI

AF:

0.0121

Gnomad AMR

AF:

0.0337

Gnomad ASJ

AF:

0.0118

Gnomad EAS

AF:

0.00212

Gnomad SAS

AF:

0.0437

Gnomad FIN

AF:

0.00348

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.0105

Gnomad OTH

AF:

0.0664

GnomAD4 exome

AF:

0.0244

AC:

AN:

164

Hom.:

Cov.:

AF XY:

0.0400

AC XY:

AN XY:

100

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AF:

0.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0278

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.0856

AC:

13031

AN:

152208

Hom.:

1611

Cov.:

AF XY:

0.0828

AC XY:

6167

AN XY:

74438

show subpopulations

African (AFR)

AF:

0.273

AC:

11340

AN:

41474

American (AMR)

AF:

0.0336

AC:

514

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0118

AC:

AN:

3470

East Asian (EAS)

AF:

0.00212

AC:

AN:

5180

South Asian (SAS)

AF:

0.0437

AC:

211

AN:

4826

European-Finnish (FIN)

AF:

0.00348

AC:

AN:

10618

Middle Eastern (MID)

AF:

0.0510

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0105

AC:

711

AN:

68026

Other (OTH)

AF:

0.0662

AC:

140

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

498

996

1494

1992

2490

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

126

252

378

504

630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0424

Hom.:

278

Bravo

AF:

0.0954

Asia WGS

AF:

0.0400

AC:

138

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

4.9

(source)

DANN

Benign

0.50

PhyloP100

-0.11

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over