chr2-112236575-C-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032494.3(ZC3H8):c.491G>T(p.Gly164Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000692 in 1,613,470 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G164D) has been classified as Benign.
Frequency
Consequence
NM_032494.3 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 |
---|---|---|---|---|---|---|---|---|
ZC3H8 | NM_032494.3 | c.491G>T | p.Gly164Val | missense_variant | Exon 4 of 9 | ENST00000409573.7 | NP_115883.2 | |
ZC3H8 | XR_001738994.2 | n.552G>T | non_coding_transcript_exon_variant | Exon 4 of 9 | ||||
FBLN7 | XR_007069507.1 | n.10509-2546C>A | intron_variant | Intron 8 of 9 | ||||
FBLN7 | XR_007069508.1 | n.10508+5690C>A | intron_variant | Intron 8 of 8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZC3H8 | ENST00000409573.7 | c.491G>T | p.Gly164Val | missense_variant | Exon 4 of 9 | 5 | NM_032494.3 | ENSP00000386488.1 | ||
ZC3H8 | ENST00000466259.1 | n.398G>T | non_coding_transcript_exon_variant | Exon 2 of 4 | 2 | |||||
ZC3H8 | ENST00000474234.5 | n.671G>T | non_coding_transcript_exon_variant | Exon 5 of 7 | 5 | |||||
ZC3H8 | ENST00000464305.1 | n.*11G>T | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.00381 AC: 580AN: 152184Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.000845 AC: 210AN: 248586Hom.: 0 AF XY: 0.000556 AC XY: 75AN XY: 134870
GnomAD4 exome AF: 0.000368 AC: 537AN: 1461168Hom.: 1 Cov.: 30 AF XY: 0.000297 AC XY: 216AN XY: 726872
GnomAD4 genome AF: 0.00381 AC: 580AN: 152302Hom.: 3 Cov.: 32 AF XY: 0.00337 AC XY: 251AN XY: 74470
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at