chr11-76351044-C-T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_004705.4(THAP12):c.2106G>A(p.Lys702Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
THAP12
NM_004705.4 synonymous
NM_004705.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.235
Publications
0 publications found
Genes affected
THAP12 (HGNC:9440): (THAP domain containing 12) Predicted to enable DNA binding activity; metal ion binding activity; and protein dimerization activity. Predicted to be involved in negative regulation of cell population proliferation and signal transduction. Predicted to be located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
THAP12 Gene-Disease associations (from GenCC):
- syndromic complex neurodevelopmental disorderInheritance: AR Classification: LIMITED Submitted by: Broad Center for Mendelian Genomics
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BP6
Variant 11-76351044-C-T is Benign according to our data. Variant chr11-76351044-C-T is described in CliVar as Likely_benign. Clinvar id is 2642165.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-76351044-C-T is described in CliVar as Likely_benign. Clinvar id is 2642165.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-76351044-C-T is described in CliVar as Likely_benign. Clinvar id is 2642165.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-76351044-C-T is described in CliVar as Likely_benign. Clinvar id is 2642165.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.235 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
THAP12 | NM_004705.4 | c.2106G>A | p.Lys702Lys | synonymous_variant | Exon 5 of 5 | ENST00000260045.8 | NP_004696.2 | |
THAP12 | NR_130898.2 | n.2497G>A | non_coding_transcript_exon_variant | Exon 6 of 6 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000160 AC: 4AN: 250748 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
4
AN:
250748
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000480 AC: 7AN: 1459244Hom.: 0 Cov.: 31 AF XY: 0.00000551 AC XY: 4AN XY: 725948 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
7
AN:
1459244
Hom.:
Cov.:
31
AF XY:
AC XY:
4
AN XY:
725948
show subpopulations
⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
1
AN:
33266
American (AMR)
AF:
AC:
0
AN:
44678
Ashkenazi Jewish (ASJ)
AF:
AC:
1
AN:
26050
East Asian (EAS)
AF:
AC:
0
AN:
39698
South Asian (SAS)
AF:
AC:
1
AN:
86160
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
4126
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1111680
Other (OTH)
AF:
AC:
0
AN:
60166
⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.000000), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.254
Heterozygous variant carriers
0
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Nov 01, 2022
CeGaT Center for Human Genetics Tuebingen
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
THAP12: BP4, BP7 -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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