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GeneBe

5-748498-A-G

Variant summary

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

The NM_001351303.2(ZDHHC11B):c.690T>C(p.Thr230=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00099 in 1,363,106 control chromosomes in the GnomAD database, including 300 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00093 ( 21 hom., cov: 25)
Exomes 𝑓: 0.0010 ( 279 hom. )

Consequence

ZDHHC11B
NM_001351303.2 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.41
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.97).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 5-748498-A-G is Benign according to our data. Variant chr5-748498-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 2655254.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-2.41 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High Homozygotes in GnomAd at 21 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ZDHHC11BNM_001351303.2 linkuse as main transcriptc.690T>C p.Thr230= synonymous_variant 8/14 ENST00000508859.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ZDHHC11BENST00000508859.8 linkuse as main transcriptc.690T>C p.Thr230= synonymous_variant 8/145 NM_001351303.2 P1
ZDHHC11BENST00000622126.2 linkuse as main transcriptn.156T>C non_coding_transcript_exon_variant 2/25
ZDHHC11BENST00000522356.3 linkuse as main transcriptc.*691T>C 3_prime_UTR_variant, NMD_transcript_variant 9/162

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000926
AC:
119
AN:
128528
Hom.:
21
Cov.:
25
show subpopulations
Gnomad AFR
AF:
0.000812
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000903
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00128
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000232
Gnomad MID
AF:
0.0108
Gnomad NFE
AF:
0.00114
Gnomad OTH
AF:
0.00114
GnomAD3 exomes
AF:
0.000860
AC:
172
AN:
199896
Hom.:
43
AF XY:
0.00104
AC XY:
112
AN XY:
108080
show subpopulations
Gnomad AFR exome
AF:
0.000190
Gnomad AMR exome
AF:
0.000468
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00123
Gnomad SAS exome
AF:
0.00110
Gnomad FIN exome
AF:
0.000117
Gnomad NFE exome
AF:
0.00114
Gnomad OTH exome
AF:
0.00137
GnomAD4 exome
AF:
0.000996
AC:
1230
AN:
1234478
Hom.:
279
Cov.:
32
AF XY:
0.00101
AC XY:
617
AN XY:
610602
show subpopulations
Gnomad4 AFR exome
AF:
0.000765
Gnomad4 AMR exome
AF:
0.000552
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000697
Gnomad4 SAS exome
AF:
0.00122
Gnomad4 FIN exome
AF:
0.000228
Gnomad4 NFE exome
AF:
0.00103
Gnomad4 OTH exome
AF:
0.00135
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000933
AC:
120
AN:
128628
Hom.:
21
Cov.:
25
AF XY:
0.000806
AC XY:
50
AN XY:
62070
show subpopulations
Gnomad4 AFR
AF:
0.000835
Gnomad4 AMR
AF:
0.000903
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00128
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000232
Gnomad4 NFE
AF:
0.00114
Gnomad4 OTH
AF:
0.00114

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 TuebingenFeb 01, 2023ZDHHC11B: BP4, BP7, BS2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.97
Cadd
Benign
1.7
Dann
Benign
0.34

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs189921796; hg19: chr5-748613; API