rs8176070

chr5-60541649-G-Achr5-60541649-G-Cchr5-60541649-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_024617.1(PART1):n.940-4453G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.263 in 151,948 control chromosomes in the GnomAD database, including 6,361 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 0.26 (6361 hom., cov: 32)
• Consequence: PART1 NR_024617.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PART1	NR_024617.1	n.940-4453G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PART1	ENST00000506884.2	n.529-4453G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.263 AC: 39871 AN: 151830 Hom.: 6346 Cov.: 32

Gnomad AFR AF: 0.0787

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.429

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.260

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.263 AC: 39891 AN: 151948 Hom.: 6361 Cov.: 32 AF XY: 0.267 AC XY: 19823 AN XY: 74258

Gnomad4 AFR AF: 0.0785

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.430

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.343

Gnomad4 OTH AF: 0.268

Alfa AF: 0.326 Hom.: 8350

Bravo AF: 0.246

Asia WGS AF: 0.334 AC: 1158 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	0.16
Dann	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8176070; hg19: chr5-59837476; COSMIC: COSV72445098;