chrX-153421516-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001136273.2(ZFP92):c.1139C>T(p.Thr380Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000965 in 1,139,403 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001136273.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZFP92 | NM_001136273.2 | c.1139C>T | p.Thr380Met | missense_variant | 6/6 | ENST00000338647.7 | |
ZFP92 | NM_001386944.1 | c.1139C>T | p.Thr380Met | missense_variant | 5/5 | ||
ZFP92 | NM_001386945.1 | c.1139C>T | p.Thr380Met | missense_variant | 7/7 | ||
ZFP92 | NM_001386943.1 | c.1013C>T | p.Thr338Met | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZFP92 | ENST00000338647.7 | c.1139C>T | p.Thr380Met | missense_variant | 6/6 | 5 | NM_001136273.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000176 AC: 2AN: 113483Hom.: 0 Cov.: 26 AF XY: 0.0000280 AC XY: 1AN XY: 35751
GnomAD4 exome AF: 0.00000877 AC: 9AN: 1025874Hom.: 0 Cov.: 31 AF XY: 0.00000904 AC XY: 3AN XY: 331824
GnomAD4 genome AF: 0.0000176 AC: 2AN: 113529Hom.: 0 Cov.: 26 AF XY: 0.0000279 AC XY: 1AN XY: 35807
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.1139C>T (p.T380M) alteration is located in exon 4 (coding exon 4) of the ZFP92 gene. This alteration results from a C to T substitution at nucleotide position 1139, causing the threonine (T) at amino acid position 380 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