chr22-29048471-A-G
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM1PP3BS2
The NM_001206998.2(ZNRF3):āc.995A>Gā(p.His332Arg) variant causes a missense change. The variant allele was found at a frequency of 0.000013 in 1,613,924 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 (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H332D) has been classified as Uncertain significance.
Frequency
Consequence
NM_001206998.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNRF3 | NM_001206998.2 | c.995A>G | p.His332Arg | missense_variant | 7/9 | ENST00000544604.7 | |
ZNRF3 | NM_032173.4 | c.695A>G | p.His232Arg | missense_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNRF3 | ENST00000544604.7 | c.995A>G | p.His332Arg | missense_variant | 7/9 | 1 | NM_001206998.2 | A2 | |
ZNRF3 | ENST00000406323.3 | c.695A>G | p.His232Arg | missense_variant | 6/8 | 1 | P2 | ||
ZNRF3 | ENST00000402174.5 | c.695A>G | p.His232Arg | missense_variant | 7/9 | 2 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152120Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249452Hom.: 0 AF XY: 0.00000739 AC XY: 1AN XY: 135352
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461804Hom.: 0 Cov.: 30 AF XY: 0.00000963 AC XY: 7AN XY: 727210
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152120Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 08, 2022 | The c.995A>G (p.H332R) alteration is located in exon 7 (coding exon 7) of the ZNRF3 gene. This alteration results from a A to G substitution at nucleotide position 995, causing the histidine (H) at amino acid position 332 to be replaced by an arginine (R). 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