Variant rs3857233 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.152

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PART1	NR_028509.1 link	n.2265C>T		non_coding_transcript_exon_variant	2/2
PART1	NR_024617.1 link	n.712-6612C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
PART1	ENST00000504876.2 link	n.1990C>T	non_coding_transcript_exon_variant	2/2	2
PART1	ENST00000661844.1 link	n.2404C>T	non_coding_transcript_exon_variant	2/2
PART1	ENST00000673825.1 link	n.2034C>T	non_coding_transcript_exon_variant	2/5

Frequencies

GnomAD3 genomes

AF:

0.0855

AC:

13005

AN:

152146

Hom.:

1596

Cov.:

show subpopulations

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:

AN:

314

Hom.:

Cov.:

AF XY:

0.0129

AC XY:

AN XY:

232

show subpopulations

Gnomad4 AFR exome

AF:

0.167

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00901

Gnomad4 OTH exome

AF:

0.0455

GnomAD4 genome

AF:

0.0857

AC:

13054

AN:

152264

Hom.:

1610

Cov.:

AF XY:

0.0830

AC XY:

6181

AN XY:

74462

show subpopulations

Gnomad4 AFR

AF:

0.274

Gnomad4 AMR

AF:

0.0337

Gnomad4 ASJ

AF:

0.0118

Gnomad4 EAS

AF:

0.00212

Gnomad4 SAS

AF:

0.0439

Gnomad4 FIN

AF:

0.00348

Gnomad4 NFE

AF:

0.0105

Gnomad4 OTH

AF:

0.0655

Alfa

AF:

0.0606

Hom.:

165

Bravo

AF:

0.0955

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

-0.81

CADD

Benign

2.3

DANN

Benign

0.33

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over