chr2-218638604-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001379659.1(ZNF142):c.5399G>A(p.Arg1800His) variant causes a missense change. The variant allele was found at a frequency of 0.0000304 in 1,613,850 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. R1800C) has been classified as Likely benign.
Frequency
Consequence
NM_001379659.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF142 | NM_001379659.1 | c.5399G>A | p.Arg1800His | missense_variant | 11/11 | ENST00000411696.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF142 | ENST00000411696.7 | c.5399G>A | p.Arg1800His | missense_variant | 11/11 | 5 | NM_001379659.1 | P1 | |
ZNF142 | ENST00000449707.5 | c.4799G>A | p.Arg1600His | missense_variant | 10/10 | 1 | |||
ZNF142 | ENST00000450765.5 | c.*4624G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 1 | ||||
ZNF142 | ENST00000433921.5 | c.*4624G>A | 3_prime_UTR_variant, NMD_transcript_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152232Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000723 AC: 18AN: 248804Hom.: 0 AF XY: 0.0000815 AC XY: 11AN XY: 134956
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461500Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 726998
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152350Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74496
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 24, 2023 | The c.4799G>A (p.R1600H) alteration is located in exon 10 (coding exon 7) of the ZNF142 gene. This alteration results from a G to A substitution at nucleotide position 4799, causing the arginine (R) at amino acid position 1600 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