rs8176070

Variant names:

• chr5-60541649-G-A
• rs8176070
• ENST00000814617.1:n.487C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-60541649-G-A
• chr5-60541649-G-C
• chr5-60541649-G-T

Variant summary

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

The ENST00000814617.1(ENSG00000305990):​n.487C>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 0.263 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: ENSG00000305990 ENST00000814617.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 10 publications found

Genes affected

ENSG00000305990 (HGNC:):

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=-0.81).
• 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 rank	MANE	Protein	UniProt
PART1	NR_024617.1	n.940-4453G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305990	ENST00000814617.1	n.487C>T		non_coding_transcript_exon_variant	Exon 1 of 1
PART1	ENST00000506884.2	n.529-4453G>A		intron_variant	Intron 3 of 3	2
PART1	ENST00000663388.1	n.498-1001G>A		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.0785 AC: 3255 AN: 41466

American (AMR) AF: 0.286 AC: 4371 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3466

East Asian (EAS) AF: 0.203 AC: 1047 AN: 5162

South Asian (SAS) AF: 0.430 AC: 2066 AN: 4810

European-Finnish (FIN) AF: 0.369 AC: 3879 AN: 10510

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

European-Non Finnish (NFE) AF: 0.343 AC: 23302 AN: 67950

Other (OTH) AF: 0.268 AC: 566 AN: 2114

Alfa AF: 0.313 Hom.: 11542

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
PhyloP100		-1.5

Splicing

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

Other links and lift over

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