16-72787445-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_006885.4(ZFHX3):c.10831C>T(p.His3611Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00786 in 1,604,088 control chromosomes in the GnomAD database, including 78 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0063 ( 8 hom., cov: 28)
Exomes 𝑓: 0.0080 ( 70 hom. )
Consequence
ZFHX3
NM_006885.4 missense
NM_006885.4 missense
Scores
4
14
Clinical Significance
Conservation
PhyloP100: 4.07
Genes affected
ZFHX3 (HGNC:777): (zinc finger homeobox 3) This gene encodes a transcription factor with multiple homeodomains and zinc finger motifs, and regulates myogenic and neuronal differentiation. The encoded protein suppresses expression of the alpha-fetoprotein gene by binding to an AT-rich enhancer motif. The protein has also been shown to negatively regulate c-Myb, and transactivate the cell cycle inhibitor cyclin-dependent kinase inhibitor 1A (also known as p21CIP1). This gene is reported to function as a tumor suppressor in several cancers, and sequence variants of this gene are also associated with atrial fibrillation. Multiple transcript variants expressed from alternate promoters and encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0062671006).
BP6
Variant 16-72787445-G-A is Benign according to our data. Variant chr16-72787445-G-A is described in ClinVar as [Benign]. Clinvar id is 769903.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00627 (952/151832) while in subpopulation AMR AF= 0.0132 (202/15274). AF 95% confidence interval is 0.0117. There are 8 homozygotes in gnomad4. There are 473 alleles in male gnomad4 subpopulation. Median coverage is 28. This position pass quality control queck.
BS2
High AC in GnomAd4 at 952 AD gene.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00625 AC: 948AN: 151720Hom.: 8 Cov.: 28
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GnomAD3 exomes AF: 0.00724 AC: 1707AN: 235666Hom.: 10 AF XY: 0.00700 AC XY: 901AN XY: 128790
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GnomAD4 exome AF: 0.00803 AC: 11661AN: 1452256Hom.: 70 Cov.: 37 AF XY: 0.00788 AC XY: 5681AN XY: 721234
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GnomAD4 genome AF: 0.00627 AC: 952AN: 151832Hom.: 8 Cov.: 28 AF XY: 0.00637 AC XY: 473AN XY: 74214
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
ZFHX3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 06, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
.;T;T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;L
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.
REVEL
Benign
Sift
Uncertain
D;D;.
Sift4G
Uncertain
T;T;.
Polyphen
P;.;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at