Genetic Variant ZDHHC20P2:n.393A>G (chr6-31380803-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 ENST00000424108.1(ZDHHC20P2):n.393A>G 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 0.612 in 151,954 control chromosomes in the GnomAD database, including 29,126 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 0.61 ( 29121 hom., cov: 31)

Exomes 𝑓: 0.81 ( 5 hom. )

Consequence

ZDHHC20P2
ENST00000424108.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.331

Publications

19 publications found

Variant links:

Genes affected

ZDHHC20P2 (HGNC:33457): (zinc finger DHHC-type containing 20 pseudogene 2)

ZDHHC20P2 links:

ENSG00000298426 (HGNC:):

ENSG00000298426 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=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.652 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC20P2		n.31380803A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC20P2	ENST00000424108.1 link	n.393A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298426	ENST00000755446.1 link	n.327-1177A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.612

AC:

92960

AN:

151820

Hom.:

29087

Cov.:

show subpopulations

Gnomad AFR

AF:

0.492

Gnomad AMI

AF:

0.883

Gnomad AMR

AF:

0.651

Gnomad ASJ

AF:

0.738

Gnomad EAS

AF:

0.612

Gnomad SAS

AF:

0.671

Gnomad FIN

AF:

0.701

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.649

Gnomad OTH

AF:

0.598

GnomAD4 exome

AF:

0.813

AC:

AN:

Hom.:

Cov.:

AF XY:

0.700

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.500

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.857

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.542

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.612

AC:

93040

AN:

151938

Hom.:

29121

Cov.:

AF XY:

0.615

AC XY:

45663

AN XY:

74252

show subpopulations

African (AFR)

AF:

0.492

AC:

20350

AN:

41394

American (AMR)

AF:

0.652

AC:

9964

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.738

AC:

2560

AN:

3470

East Asian (EAS)

AF:

0.612

AC:

3165

AN:

5168

South Asian (SAS)

AF:

0.672

AC:

3228

AN:

4806

European-Finnish (FIN)

AF:

0.701

AC:

7405

AN:

10556

Middle Eastern (MID)

AF:

0.653

AC:

192

AN:

294

European-Non Finnish (NFE)

AF:

0.649

AC:

44102

AN:

67950

Other (OTH)

AF:

0.602

AC:

1269

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1737

3473

5210

6946

8683

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.638

Hom.:

130908

Bravo

AF:

0.600

Asia WGS

AF:

0.663

AC:

2307

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

5.7

(source)

DANN

Benign

0.41

PhyloP100

0.33

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over