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
NM_001351303.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.189
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 |
---|---|---|---|---|---|---|---|---|
ZDHHC11B | NM_001351303.2 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
ZDHHC11B | ENST00000508859.8 | c.1014G>A | p.Ser338Ser | synonymous_variant | 11/14 | 5 | NM_001351303.2 | ENSP00000442373.2 | ||
ZDHHC11B | ENST00000522356.3 | n.*1015G>A | non_coding_transcript_exon_variant | 12/16 | 2 | ENSP00000505988.1 | ||||
ZDHHC11B | ENST00000522356.3 | n.*1015G>A | 3_prime_UTR_variant | 12/16 | 2 | ENSP00000505988.1 |
Frequencies
GnomAD3 genomes AF: 0.000277 AC: 42AN: 151378Hom.: 1 Cov.: 35
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GnomAD3 exomes AF: 0.000216 AC: 54AN: 249786Hom.: 0 AF XY: 0.000252 AC XY: 34AN XY: 135112
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GnomAD4 exome AF: 0.000274 AC: 400AN: 1459498Hom.: 7 Cov.: 31 AF XY: 0.000285 AC XY: 207AN XY: 726200
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GnomAD4 genome AF: 0.000290 AC: 44AN: 151496Hom.: 1 Cov.: 35 AF XY: 0.000230 AC XY: 17AN XY: 74034
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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 submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2024 | ZDHHC11B: BP4, BP7 - |
Computational scores
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Benign
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DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at