17-82832512-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_024702.3(ZNF750):c.-58C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 1,487,512 control chromosomes in the GnomAD database, including 22,965 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.17 ( 2308 hom., cov: 32)
Exomes 𝑓: 0.17 ( 20657 hom. )
Consequence
ZNF750
NM_024702.3 5_prime_UTR
NM_024702.3 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.497
Publications
12 publications found
Genes affected
ZNF750 (HGNC:25843): (zinc finger protein 750) This gene encodes a protein with a nuclear localization site and a C2H2 zinc finger domain. Mutations in this gene have been associated with seborrhea-like dermatitis with psoriasiform elements. [provided by RefSeq, Jul 2008]
TBCD (HGNC:11581): (tubulin folding cofactor D) Cofactor D is one of four proteins (cofactors A, D, E, and C) involved in the pathway leading to correctly folded beta-tubulin from folding intermediates. Cofactors A and D are believed to play a role in capturing and stabilizing beta-tubulin intermediates in a quasi-native confirmation. Cofactor E binds to the cofactor D/beta-tubulin complex; interaction with cofactor C then causes the release of beta-tubulin polypeptides that are committed to the native state. [provided by RefSeq, Jul 2008]
TBCD Gene-Disease associations (from GenCC):
- early-onset progressive diffuse brain atrophy-microcephaly-muscle weakness-optic atrophy syndromeInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae)
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BP6
Variant 17-82832512-G-A is Benign according to our data. Variant chr17-82832512-G-A is described in ClinVar as [Benign]. Clinvar id is 1227535.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.167 AC: 25405AN: 151974Hom.: 2305 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
25405
AN:
151974
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.169 AC: 226190AN: 1335420Hom.: 20657 Cov.: 21 AF XY: 0.165 AC XY: 110900AN XY: 670752 show subpopulations
GnomAD4 exome
AF:
AC:
226190
AN:
1335420
Hom.:
Cov.:
21
AF XY:
AC XY:
110900
AN XY:
670752
show subpopulations
African (AFR)
AF:
AC:
4009
AN:
31112
American (AMR)
AF:
AC:
12467
AN:
43860
Ashkenazi Jewish (ASJ)
AF:
AC:
3485
AN:
25384
East Asian (EAS)
AF:
AC:
2881
AN:
39130
South Asian (SAS)
AF:
AC:
4277
AN:
83680
European-Finnish (FIN)
AF:
AC:
9163
AN:
40096
Middle Eastern (MID)
AF:
AC:
552
AN:
5546
European-Non Finnish (NFE)
AF:
AC:
180183
AN:
1010066
Other (OTH)
AF:
AC:
9173
AN:
56546
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.497
Heterozygous variant carriers
0
9506
19013
28519
38026
47532
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
5968
11936
17904
23872
29840
<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: 0.167 AC: 25426AN: 152092Hom.: 2308 Cov.: 32 AF XY: 0.167 AC XY: 12411AN XY: 74358 show subpopulations
GnomAD4 genome
AF:
AC:
25426
AN:
152092
Hom.:
Cov.:
32
AF XY:
AC XY:
12411
AN XY:
74358
show subpopulations
African (AFR)
AF:
AC:
5426
AN:
41468
American (AMR)
AF:
AC:
3510
AN:
15278
Ashkenazi Jewish (ASJ)
AF:
AC:
494
AN:
3466
East Asian (EAS)
AF:
AC:
427
AN:
5184
South Asian (SAS)
AF:
AC:
206
AN:
4828
European-Finnish (FIN)
AF:
AC:
2447
AN:
10580
Middle Eastern (MID)
AF:
AC:
30
AN:
294
European-Non Finnish (NFE)
AF:
AC:
12356
AN:
67974
Other (OTH)
AF:
AC:
312
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1078
2156
3234
4312
5390
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
262
524
786
1048
1310
<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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
210
AN:
3478
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
May 15, 2021
GeneDx
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
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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