chrX-65503035-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001010888.4(ZC3H12B):c.2337G>A(p.Met779Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000237 in 1,209,280 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 77 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001010888.4 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 |
---|---|---|---|---|---|---|---|
ZC3H12B | NM_001010888.4 | c.2337G>A | p.Met779Ile | missense_variant | 10/10 | ENST00000338957.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H12B | ENST00000338957.5 | c.2337G>A | p.Met779Ile | missense_variant | 10/10 | 1 | NM_001010888.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000135 AC: 15AN: 111126Hom.: 0 Cov.: 23 AF XY: 0.0000601 AC XY: 2AN XY: 33302
GnomAD3 exomes AF: 0.000121 AC: 22AN: 181428Hom.: 0 AF XY: 0.000119 AC XY: 8AN XY: 67396
GnomAD4 exome AF: 0.000248 AC: 272AN: 1098104Hom.: 0 Cov.: 31 AF XY: 0.000206 AC XY: 75AN XY: 363530
GnomAD4 genome ? AF: 0.000135 AC: 15AN: 111176Hom.: 0 Cov.: 23 AF XY: 0.0000599 AC XY: 2AN XY: 33362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 14, 2022 | The c.2337G>A (p.M779I) alteration is located in exon 5 (coding exon 5) of the ZC3H12B gene. This alteration results from a G to A substitution at nucleotide position 2337, causing the methionine (M) at amino acid position 779 to be replaced by an isoleucine (I). 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