rs4133470

Variant names:

• chr5-60522419-T-C
• rs4133470
• ENST00000504876.2:n.1617T>C

Variant summary

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

The ENST00000504876.2(PART1):​n.1617T>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 0.385 in 152,064 control chromosomes in the GnomAD database, including 15,576 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 0.38 (15575 hom., cov: 32)
  • Exomes 𝑓: 0.29 (1 hom.)
• Consequence: PART1 ENST00000504876.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.250
• Publications: 8 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.754 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PART1	NR_028509.1		n.1892T>C		non_coding_transcript_exon	Exon 2 of 2
	PART1	NR_024617.1		n.712-6985T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PART1	ENST00000504876.2	TSL:2	n.1617T>C		non_coding_transcript_exon	Exon 2 of 2
	PART1	ENST00000661844.1		n.2031T>C		non_coding_transcript_exon	Exon 2 of 2
	PART1	ENST00000673825.1		n.1661T>C		non_coding_transcript_exon	Exon 2 of 5

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58373 AN: 151932 Hom.: 15519 Cov.: 32

Gnomad AFR AF: 0.761

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.0420

Gnomad SAS AF: 0.204

Gnomad FIN AF: 0.248

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.352

GnomAD4 exome AF: 0.286 AC: 4 AN: 14 Hom.: 1 Cov.: 0 AF XY: 0.400 AC XY: 4 AN XY: 10

African (AFR) AF: 1.00 AC: 2 AN: 2

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.167 AC: 2 AN: 12

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.385 AC: 58482 AN: 152050 Hom.: 15575 Cov.: 32 AF XY: 0.376 AC XY: 27969 AN XY: 74306

African (AFR) AF: 0.761 AC: 31571 AN: 41466

American (AMR) AF: 0.243 AC: 3708 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1089 AN: 3466

East Asian (EAS) AF: 0.0419 AC: 217 AN: 5182

South Asian (SAS) AF: 0.204 AC: 981 AN: 4814

European-Finnish (FIN) AF: 0.248 AC: 2621 AN: 10562

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17303 AN: 67962

Other (OTH) AF: 0.349 AC: 735 AN: 2106

Alfa AF: 0.288 Hom.: 18037

Bravo AF: 0.399

Asia WGS AF: 0.155 AC: 541 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.0
DANN	Benign	0.44
PhyloP100		0.25

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs4133470;

hg19: chr5-59818246;

COSMIC: COSV72259938;