8-134509638-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020863.4(ZFAT):c.3473C>T(p.Thr1158Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000102 in 1,613,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T1158T) has been classified as Benign.
Frequency
Consequence
NM_020863.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFAT | NM_020863.4 | c.3473C>T | p.Thr1158Met | missense_variant | 15/16 | ENST00000377838.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFAT | ENST00000377838.8 | c.3473C>T | p.Thr1158Met | missense_variant | 15/16 | 1 | NM_020863.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000165 AC: 25AN: 151722Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000165 AC: 41AN: 248862Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 134968
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461336Hom.: 0 Cov.: 30 AF XY: 0.0000922 AC XY: 67AN XY: 726926
GnomAD4 genome ? AF: 0.000158 AC: 24AN: 151840Hom.: 0 Cov.: 31 AF XY: 0.000108 AC XY: 8AN XY: 74154
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2022 | The c.3473C>T (p.T1158M) alteration is located in exon 15 (coding exon 15) of the ZFAT gene. This alteration results from a C to T substitution at nucleotide position 3473, causing the threonine (T) at amino acid position 1158 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at