5-60541807-A-T

Variant names:

• chr5-60541807-A-T
• rs27564
• ENST00000506884.2:n.529-4295A>T

Variant summary

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

The ENST00000506884.2(PART1):​n.529-4295A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.712 in 152,126 control chromosomes in the GnomAD database, including 39,546 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 0.71 (39546 hom., cov: 32)
• Consequence: PART1 ENST00000506884.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200

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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.872 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PART1	NR_024617.1	n.940-4295A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PART1	ENST00000506884.2	n.529-4295A>T		intron_variant	Intron 3 of 3	2
PART1	ENST00000663388.1	n.498-843A>T		intron_variant	Intron 2 of 3
PART1	ENST00000664492.1	n.376-4295A>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.712 AC: 108196 AN: 152008 Hom.: 39503 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.746

Gnomad AMR AF: 0.675

Gnomad ASJ AF: 0.719

Gnomad EAS AF: 0.578

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.570

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.708

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

GnomAD4 genome AF: 0.712 AC: 108278 AN: 152126 Hom.: 39546 Cov.: 32 AF XY: 0.701 AC XY: 52115 AN XY: 74364

Gnomad4 AFR AF: 0.880

Gnomad4 AMR AF: 0.675

Gnomad4 ASJ AF: 0.719

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.570

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.700

Alfa AF: 0.699 Hom.: 4680

Bravo AF: 0.729

Asia WGS AF: 0.538 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.4
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs27564; hg19: chr5-59837634;