dbSNP rs6795707: ZDHHC19:c.268+77C>A (chr3-196210539-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001039617.2(ZDHHC19):c.268+77C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 1,596,488 control chromosomes in the GnomAD database, including 20,077 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 0.13 ( 1646 hom., cov: 32)

Exomes 𝑓: 0.15 ( 18431 hom. )

Consequence

ZDHHC19
NM_001039617.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.537

Publications

6 publications found

Variant links:

Genes affected

ZDHHC19 (HGNC:20713): (zinc finger DHHC-type palmitoyltransferase 19) Enables protein-cysteine S-palmitoyltransferase activity. Involved in peptidyl-L-cysteine S-palmitoylation. Located in Golgi membrane; endoplasmic reticulum; and perinucleolar compartment. [provided by Alliance of Genome Resources, Apr 2022]

ZDHHC19 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.338 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001039617.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZDHHC19	NM_001039617.2	MANE Select	c.268+77C>A	intron	N/A	NP_001034706.1	Q8WVZ1-1
ZDHHC19	NR_135617.2		n.353+77C>A	intron	N/A
ZDHHC19	NR_135618.2		n.353+77C>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ZDHHC19	ENST00000296326.8	TSL:5 MANE Select	c.268+77C>A	intron	N/A	ENSP00000296326.3	Q8WVZ1-1
ZDHHC19	ENST00000397544.6	TSL:1	n.268+77C>A	intron	N/A	ENSP00000380678.2	Q8WVZ1-3
ZDHHC19	ENST00000465519.5	TSL:1	n.261+77C>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.125

AC:

19050

AN:

152116

Hom.:

1648

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0353

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.196

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.351

Gnomad SAS

AF:

0.201

Gnomad FIN

AF:

0.146

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.137

Gnomad OTH

AF:

0.127

GnomAD4 exome

AF:

0.153

AC:

221293

AN:

1444254

Hom.:

18431

AF XY:

0.154

AC XY:

110185

AN XY:

717706

show subpopulations

African (AFR)

AF:

0.0291

AC:

963

AN:

33102

American (AMR)

AF:

0.238

AC:

10418

AN:

43764

Ashkenazi Jewish (ASJ)

AF:

0.144

AC:

3631

AN:

25198

East Asian (EAS)

AF:

0.343

AC:

13529

AN:

39482

South Asian (SAS)

AF:

0.187

AC:

15729

AN:

83944

European-Finnish (FIN)

AF:

0.140

AC:

7329

AN:

52170

Middle Eastern (MID)

AF:

0.150

AC:

843

AN:

5628

European-Non Finnish (NFE)

AF:

0.145

AC:

159547

AN:

1101334

Other (OTH)

AF:

0.156

AC:

9304

AN:

59632

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

9366

18731

28097

37462

46828

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

5912

11824

17736

23648

29560

<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:

0.125

AC:

19039

AN:

152234

Hom.:

1646

Cov.:

AF XY:

0.129

AC XY:

9602

AN XY:

74434

show subpopulations

African (AFR)

AF:

0.0352

AC:

1463

AN:

41562

American (AMR)

AF:

0.196

AC:

3001

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

489

AN:

3470

East Asian (EAS)

AF:

0.351

AC:

1813

AN:

5158

South Asian (SAS)

AF:

0.201

AC:

972

AN:

4824

European-Finnish (FIN)

AF:

0.146

AC:

1542

AN:

10594

Middle Eastern (MID)

AF:

0.146

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.137

AC:

9346

AN:

68014

Other (OTH)

AF:

0.125

AC:

264

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

808

1616

2425

3233

4041

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

232

464

696

928

1160

<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:

0.136

Hom.:

833

Bravo

AF:

0.128

Asia WGS

AF:

0.217

AC:

754

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

5.8

(source)

DANN

Benign

0.53

PhyloP100

0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over