dbSNP rs4143332: ZDHHC20P2:n.178G>A (chr6-31380588-G-A) – 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.178G>A 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 0.0814 in 142,182 control chromosomes in the GnomAD database, including 592 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 0.081 ( 589 hom., cov: 33)

Exomes 𝑓: 0.15 ( 3 hom. )

Consequence

ZDHHC20P2
ENST00000424108.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100

Publications

26 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=-0.91).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ZDHHC20P2		n.31380588G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ZDHHC20P2	ENST00000424108.1 link	n.178G>A		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000298426	ENST00000755446.1 link	n.327-1392G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0814

AC:

11545

AN:

141914

Hom.:

589

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0390

Gnomad AMI

AF:

0.154

Gnomad AMR

AF:

0.0413

Gnomad ASJ

AF:

0.0482

Gnomad EAS

AF:

0.00545

Gnomad SAS

AF:

0.0707

Gnomad FIN

AF:

0.0875

Gnomad MID

AF:

0.0327

Gnomad NFE

AF:

0.121

Gnomad OTH

AF:

0.0626

GnomAD4 exome

AF:

0.147

AC:

AN:

150

Hom.:

Cov.:

AF XY:

0.122

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.500

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.0333

AC:

AN:

Middle Eastern (MID)

AF:

0.111

AC:

AN:

European-Non Finnish (NFE)

AF:

0.212

AC:

AN:

Other (OTH)

AF:

0.100

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.544

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.0813

AC:

11549

AN:

142032

Hom.:

589

Cov.:

AF XY:

0.0774

AC XY:

5321

AN XY:

68736

show subpopulations

African (AFR)

AF:

0.0390

AC:

1487

AN:

38140

American (AMR)

AF:

0.0412

AC:

566

AN:

13736

Ashkenazi Jewish (ASJ)

AF:

0.0482

AC:

158

AN:

3278

East Asian (EAS)

AF:

0.00525

AC:

AN:

4572

South Asian (SAS)

AF:

0.0720

AC:

299

AN:

4152

European-Finnish (FIN)

AF:

0.0875

AC:

824

AN:

9414

Middle Eastern (MID)

AF:

0.0315

AC:

AN:

286

European-Non Finnish (NFE)

AF:

0.121

AC:

7929

AN:

65660

Other (OTH)

AF:

0.0619

AC:

119

AN:

1924

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

532

1064

1596

2128

2660

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

142

284

426

568

710

<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:

0.111

Hom.:

2529

Bravo

AF:

0.0700

Asia WGS

AF:

0.0210

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

8.8

(source)

DANN

Benign

0.49

PhyloP100

-0.010

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