rs1393669125
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_080660.4(ZC3HAV1L):c.336G>T(p.Met112Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000302 in 1,324,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.
Frequency
Consequence
NM_080660.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZC3HAV1L | NM_080660.4 | c.336G>T | p.Met112Ile | missense_variant | Exon 1 of 5 | ENST00000275766.2 | NP_542391.2 | |
ZC3HAV1L | XM_011516688.4 | c.336G>T | p.Met112Ile | missense_variant | Exon 1 of 5 | XP_011514990.1 | ||
ZC3HAV1L | XM_006716176.4 | c.336G>T | p.Met112Ile | missense_variant | Exon 1 of 4 | XP_006716239.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000400 AC: 3AN: 75002Hom.: 0 AF XY: 0.0000462 AC XY: 2AN XY: 43250
GnomAD4 exome AF: 0.00000302 AC: 4AN: 1324042Hom.: 0 Cov.: 34 AF XY: 0.00000613 AC XY: 4AN XY: 652484
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at