19-55593325-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2

The NM_032836.3(FIZ1):​c.616G>A​(p.Ala206Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,282,356 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000027 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000013 ( 0 hom. )

Consequence

FIZ1
NM_032836.3 missense

Scores

1
4
14

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.879
Variant links:
Genes affected
FIZ1 (HGNC:25917): (FLT3 interacting zinc finger 1) This gene encodes zinc finger protein, which interacts with a receptor tyrosine kinase involved in the regulation of hematopoietic and lymphoid cells. This gene product also interacts with a transcription factor that regulates the expression of rod-specific genes in retina. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -6 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.17557326).
BS2
High AC in GnomAdExome4 at 15 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FIZ1NM_032836.3 linkc.616G>A p.Ala206Thr missense_variant 3/3 ENST00000221665.5 NP_116225.2
FIZ1XM_005259352.5 linkc.616G>A p.Ala206Thr missense_variant 3/3 XP_005259409.1 Q96SL8
FIZ1XM_047439564.1 linkc.616G>A p.Ala206Thr missense_variant 2/2 XP_047295520.1
FIZ1XM_011527426.3 linkc.598G>A p.Ala200Thr missense_variant 2/2 XP_011525728.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FIZ1ENST00000221665.5 linkc.616G>A p.Ala206Thr missense_variant 3/31 NM_032836.3 ENSP00000221665.2 Q96SL8
FIZ1ENST00000590714.1 linkc.*35G>A downstream_gene_variant 1 ENSP00000465131.1 K7EJE2

Frequencies

GnomAD3 genomes
AF:
0.0000267
AC:
4
AN:
150028
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000594
Gnomad OTH
AF:
0.00
GnomAD4 exome
AF:
0.0000132
AC:
15
AN:
1132328
Hom.:
0
Cov.:
33
AF XY:
0.00000914
AC XY:
5
AN XY:
547026
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000376
Gnomad4 NFE exome
AF:
0.0000148
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
AF:
0.0000267
AC:
4
AN:
150028
Hom.:
0
Cov.:
32
AF XY:
0.0000547
AC XY:
4
AN XY:
73192
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000594
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000302
ExAC
AF:
0.0000452
AC:
3

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsSep 13, 2023The c.616G>A (p.A206T) alteration is located in exon 3 (coding exon 2) of the FIZ1 gene. This alteration results from a G to A substitution at nucleotide position 616, causing the alanine (A) at amino acid position 206 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.16
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.55
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.058
T
Eigen
Benign
-0.49
Eigen_PC
Benign
-0.55
FATHMM_MKL
Benign
0.20
N
LIST_S2
Benign
0.54
T
M_CAP
Uncertain
0.12
D
MetaRNN
Benign
0.18
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
0.30
N
PrimateAI
Pathogenic
0.92
D
PROVEAN
Benign
-1.5
N
REVEL
Benign
0.074
Sift
Uncertain
0.024
D
Sift4G
Uncertain
0.011
D
Polyphen
0.82
P
Vest4
0.17
MutPred
0.60
Gain of phosphorylation at A206 (P = 0.0545);
MVP
0.20
ClinPred
0.21
T
GERP RS
2.4
Varity_R
0.10
gMVP
0.32

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs760668931; hg19: chr19-56104691; API