Genetic Variant YWHAZP5:n.105689046A>G (chr10-105689046-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.702 in 151,890 control chromosomes in the GnomAD database, including 37,757 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 0.70 ( 37757 hom., cov: 30)

Consequence

YWHAZP5
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.248

Publications

1 publications found

Variant links:

Genes affected

YWHAZP5 (HGNC:30564): (tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta pseudogene 5)

YWHAZP5 links:

LINC02627 (HGNC:54106): (long intergenic non-protein coding RNA 2627)

LINC02627 links:

Genome browser will be placed here

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=-1.0).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.917 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
YWHAZP5		n.105689046A>G		intragenic_variant
LINC02627	NR_120625.1 link	n.431-15358T>C		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02627	ENST00000836854.1 link	n.449-15358T>C	intron_variant	Intron 3 of 7
LINC02627	ENST00000836855.1 link	n.395-15358T>C	intron_variant	Intron 3 of 5
LINC02627	ENST00000836856.1 link	n.515-15358T>C	intron_variant	Intron 4 of 6
LINC02627	ENST00000836857.1 link	n.301-15358T>C	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.702

AC:

106579

AN:

151772

Hom.:

37744

Cov.:

show subpopulations

Gnomad AFR

AF:

0.696

Gnomad AMI

AF:

0.613

Gnomad AMR

AF:

0.702

Gnomad ASJ

AF:

0.788

Gnomad EAS

AF:

0.940

Gnomad SAS

AF:

0.545

Gnomad FIN

AF:

0.750

Gnomad MID

AF:

0.680

Gnomad NFE

AF:

0.688

Gnomad OTH

AF:

0.710

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

GnomAD4 genome

AF:

0.702

AC:

106647

AN:

151890

Hom.:

37757

Cov.:

AF XY:

0.702

AC XY:

52112

AN XY:

74248

show subpopulations

African (AFR)

AF:

0.696

AC:

28822

AN:

41404

American (AMR)

AF:

0.702

AC:

10700

AN:

15244

Ashkenazi Jewish (ASJ)

AF:

0.788

AC:

2734

AN:

3470

East Asian (EAS)

AF:

0.939

AC:

4851

AN:

5164

South Asian (SAS)

AF:

0.544

AC:

2619

AN:

4814

European-Finnish (FIN)

AF:

0.750

AC:

7910

AN:

10544

Middle Eastern (MID)

AF:

0.670

AC:

197

AN:

294

European-Non Finnish (NFE)

AF:

0.688

AC:

46759

AN:

67938

Other (OTH)

AF:

0.710

AC:

1497

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1616

3232

4847

6463

8079

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.671

Hom.:

15364

Bravo

AF:

0.707

Asia WGS

AF:

0.698

AC:

2427

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.54

(source)

DANN

Benign

0.39

PhyloP100

0.25

Splicing

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

Publications

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10-105689046-A-G

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