9-128740006-C-T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_006336.4(ZER1):c.1967G>A(p.Arg656His) variant causes a missense change. The variant allele was found at a frequency of 0.0000161 in 1,613,974 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006336.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZER1 | NM_006336.4 | c.1967G>A | p.Arg656His | missense_variant | Exon 13 of 16 | ENST00000291900.7 | NP_006327.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251442Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135890
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.0000151 AC XY: 11AN XY: 727184
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152164Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1967G>A (p.R656H) alteration is located in exon 13 (coding exon 12) of the ZER1 gene. This alteration results from a G to A substitution at nucleotide position 1967, causing the arginine (R) at amino acid position 656 to be replaced by a histidine (H). 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