Genetic Variant ENST00000528056.5:n.508-8497C>T (chrY-7295440-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000528056.5(PRKY):n.508-8497C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.15 ( 0 hom., 4979 hem., cov: 0)

Consequence

PRKY
ENST00000528056.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.468

Publications

2 publications found

Variant links:

Genes affected

PRKY (HGNC:):

PRKY links:

PRKY (HGNC:9444): (protein kinase Y-linked (pseudogene)) This gene is similar to the protein kinase, X-linked gene in the pseudoautosomal region of the X chromosome. The gene is classified as a transcribed pseudogene because it has lost a coding exon that results in all transcripts being candidates for nonsense-mediated decay (NMD) and unlikely to express a protein. Abnormal recombination between this gene and a related gene on chromosome X is a frequent cause of XX males and XY females. [provided by RefSeq, Jul 2010]

PRKY links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PRKY	NR_028062.1 link	n.508-8497C>T		intron_variant	Intron 1 of 7

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PRKY	ENST00000528056.5 link	n.508-8497C>T	intron_variant	Intron 1 of 7	1
PRKY	ENST00000533551.5 link	n.167-8497C>T	intron_variant	Intron 1 of 6	6
PRKY	ENST00000836332.1 link	n.105-8497C>T	intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.152

AC:

4946

AN:

32624

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.593

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0373

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00202

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0141

Gnomad NFE

AF:

0.00207

Gnomad OTH

AF:

0.0837

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

GnomAD4 genome

AF:

0.152

AC:

4979

AN:

32686

Hom.:

Cov.:

AF XY:

0.152

AC XY:

4979

AN XY:

32686

show subpopulations

African (AFR)

AF:

0.593

AC:

4779

AN:

8058

American (AMR)

AF:

0.0373

AC:

130

AN:

3489

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

767

East Asian (EAS)

AF:

0.00

AC:

AN:

1241

South Asian (SAS)

AF:

0.00202

AC:

AN:

1488

European-Finnish (FIN)

AF:

0.00

AC:

AN:

3380

Middle Eastern (MID)

AF:

0.0143

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00207

AC:

AN:

13518

Other (OTH)

AF:

0.0832

AC:

AN:

457

Age Distribution

Genome Hom

Variant carriers

104

156

208

260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

4.3

(source)

DANN

Benign

0.45

PhyloP100

0.47

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over