chr1-37480417-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_025079.3(ZC3H12A):c.571G>A(p.Val191Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000229 in 1,612,828 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V191G) has been classified as Uncertain significance.
Frequency
Consequence
NM_025079.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3H12A | NM_025079.3 | c.571G>A | p.Val191Met | missense_variant | 3/6 | ENST00000373087.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3H12A | ENST00000373087.7 | c.571G>A | p.Val191Met | missense_variant | 3/6 | 1 | NM_025079.3 | P1 | |
ZC3H12A | ENST00000472312.1 | n.419G>A | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
ZC3H12A | ENST00000640233.1 | c.571G>A | p.Val191Met | missense_variant, NMD_transcript_variant | 3/6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000522 AC: 13AN: 249196Hom.: 0 AF XY: 0.0000371 AC XY: 5AN XY: 134724
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1460506Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 726568
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74486
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2021 | The c.571G>A (p.V191M) alteration is located in exon 3 (coding exon 2) of the ZC3H12A gene. This alteration results from a G to A substitution at nucleotide position 571, causing the valine (V) at amino acid position 191 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