5-60525716-A-G

Variant names:

• chr5-60525716-A-G
• rs35382
• ENST00000504876.2:n.4914A>G

Variant summary

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

The ENST00000504876.2(PART1):​n.4914A>G 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 0.53 in 152,010 control chromosomes in the GnomAD database, including 21,496 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 0.53 (21496 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: PART1 ENST00000504876.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.837
• Publications: 7 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.562 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.5189A>G		non_coding_transcript_exon	Exon 2 of 2
	PART1	NR_024617.1		n.712-3688A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PART1	ENST00000504876.2	TSL:2	n.4914A>G		non_coding_transcript_exon	Exon 2 of 2
	PART1	ENST00000661844.1		n.5328A>G		non_coding_transcript_exon	Exon 2 of 2
	PART1	ENST00000506884.2	TSL:2	n.301-3688A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80516 AN: 151892 Hom.: 21489 Cov.: 33

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.637

Gnomad EAS AF: 0.572

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.601

Gnomad MID AF: 0.500

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.545

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.530 AC: 80538 AN: 152010 Hom.: 21496 Cov.: 33 AF XY: 0.530 AC XY: 39383 AN XY: 74310

African (AFR) AF: 0.477 AC: 19762 AN: 41432

American (AMR) AF: 0.572 AC: 8739 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.637 AC: 2210 AN: 3470

East Asian (EAS) AF: 0.573 AC: 2960 AN: 5170

South Asian (SAS) AF: 0.382 AC: 1841 AN: 4822

European-Finnish (FIN) AF: 0.601 AC: 6344 AN: 10550

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.542 AC: 36844 AN: 67968

Other (OTH) AF: 0.538 AC: 1136 AN: 2112

Alfa AF: 0.538 Hom.: 26431

Bravo AF: 0.531

Asia WGS AF: 0.467 AC: 1627 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		0.84

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: rs35382;

hg19: chr5-59821543;