chr7-44756468-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_031449.4(ZMIZ2):c.94G>A(p.Ala32Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,946 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_031449.4 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 |
---|---|---|---|---|---|---|---|
ZMIZ2 | NM_031449.4 | c.94G>A | p.Ala32Thr | missense_variant | 3/19 | ENST00000309315.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZMIZ2 | ENST00000309315.9 | c.94G>A | p.Ala32Thr | missense_variant | 3/19 | 2 | NM_031449.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000521 AC: 13AN: 249504Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135388
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461752Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727166
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152194Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 20, 2023 | The c.94G>A (p.A32T) alteration is located in exon 3 (coding exon 2) of the ZMIZ2 gene. This alteration results from a G to A substitution at nucleotide position 94, causing the alanine (A) at amino acid position 32 to be replaced by a threonine (T). 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