5-733761-C-T

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Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_001351303.2(ZDHHC11B):​c.1014G>A​(p.Ser338Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000276 in 1,610,994 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00029 ( 1 hom., cov: 35)
Exomes 𝑓: 0.00027 ( 7 hom. )

Consequence

ZDHHC11B
NM_001351303.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.189
Variant links:
Genes affected
ZDHHC11B (HGNC:32962): (zinc finger DHHC-type containing 11B) Predicted to enable protein-cysteine S-palmitoyltransferase activity. Predicted to be involved in several processes, including antiviral innate immune response; peptidyl-L-cysteine S-palmitoylation; and positive regulation of defense response to virus by host. Predicted to be located in endosome membrane. Predicted to be active in Golgi apparatus and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
Variant 5-733761-C-T is Benign according to our data. Variant chr5-733761-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 3388360.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.189 with no splicing effect.
BS2
High Homozygotes in GnomAdExome4 at 7 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ZDHHC11BNM_001351303.2 linkuse as main transcriptc.1014G>A p.Ser338Ser synonymous_variant 11/14 ENST00000508859.8 NP_001338232.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ZDHHC11BENST00000508859.8 linkuse as main transcriptc.1014G>A p.Ser338Ser synonymous_variant 11/145 NM_001351303.2 ENSP00000442373.2 P0C7U3
ZDHHC11BENST00000522356.3 linkuse as main transcriptn.*1015G>A non_coding_transcript_exon_variant 12/162 ENSP00000505988.1 A0A7P0TA36
ZDHHC11BENST00000522356.3 linkuse as main transcriptn.*1015G>A 3_prime_UTR_variant 12/162 ENSP00000505988.1 A0A7P0TA36

Frequencies

GnomAD3 genomes
AF:
0.000277
AC:
42
AN:
151378
Hom.:
1
Cov.:
35
show subpopulations
Gnomad AFR
AF:
0.000122
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000658
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.0000942
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000515
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000216
AC:
54
AN:
249786
Hom.:
0
AF XY:
0.000252
AC XY:
34
AN XY:
135112
show subpopulations
Gnomad AFR exome
AF:
0.0000622
Gnomad AMR exome
AF:
0.0000289
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000131
Gnomad FIN exome
AF:
0.0000481
Gnomad NFE exome
AF:
0.000415
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.000274
AC:
400
AN:
1459498
Hom.:
7
Cov.:
31
AF XY:
0.000285
AC XY:
207
AN XY:
726200
show subpopulations
Gnomad4 AFR exome
AF:
0.0000300
Gnomad4 AMR exome
AF:
0.0000448
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000928
Gnomad4 FIN exome
AF:
0.0000191
Gnomad4 NFE exome
AF:
0.000337
Gnomad4 OTH exome
AF:
0.000149
GnomAD4 genome
AF:
0.000290
AC:
44
AN:
151496
Hom.:
1
Cov.:
35
AF XY:
0.000230
AC XY:
17
AN XY:
74034
show subpopulations
Gnomad4 AFR
AF:
0.000122
Gnomad4 AMR
AF:
0.0000657
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.0000942
Gnomad4 NFE
AF:
0.000515
Gnomad4 OTH
AF:
0.000953
Alfa
AF:
0.000545
Hom.:
1
EpiCase
AF:
0.000273
EpiControl
AF:
0.000415

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenOct 01, 2024ZDHHC11B: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
1.1
DANN
Benign
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.070
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs774407835; hg19: chr5-733876; COSMIC: COSV66977900; COSMIC: COSV66977900; API