X-153418727-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001136273.2(ZFP92):c.88C>T(p.Leu30Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000635 in 1,166,205 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZFP92 | NM_001136273.2 | c.88C>T | p.Leu30Phe | missense_variant | Exon 4 of 6 | ENST00000338647.7 | NP_001129745.1 | |
ZFP92 | NM_001386944.1 | c.88C>T | p.Leu30Phe | missense_variant | Exon 3 of 5 | NP_001373873.1 | ||
ZFP92 | NM_001386945.1 | c.88C>T | p.Leu30Phe | missense_variant | Exon 5 of 7 | NP_001373874.1 | ||
ZFP92 | NM_001386943.1 | c.-39C>T | 5_prime_UTR_variant | Exon 2 of 4 | NP_001373872.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000376 AC: 42AN: 111803Hom.: 0 Cov.: 23 AF XY: 0.000265 AC XY: 9AN XY: 33973
GnomAD3 exomes AF: 0.0000951 AC: 11AN: 115718Hom.: 0 AF XY: 0.0000964 AC XY: 4AN XY: 41474
GnomAD4 exome AF: 0.0000304 AC: 32AN: 1054352Hom.: 0 Cov.: 31 AF XY: 0.0000203 AC XY: 7AN XY: 345014
GnomAD4 genome AF: 0.000375 AC: 42AN: 111853Hom.: 0 Cov.: 23 AF XY: 0.000264 AC XY: 9AN XY: 34033
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.88C>T (p.L30F) alteration is located in exon 2 (coding exon 2) of the ZFP92 gene. This alteration results from a C to T substitution at nucleotide position 88, causing the leucine (L) at amino acid position 30 to be replaced by a phenylalanine (F). 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