chr7-139055248-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020119.4(ZC3HAV1):c.2144G>A(p.Arg715His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,613,212 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. R715C) has been classified as Uncertain significance.
Frequency
Consequence
NM_020119.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZC3HAV1 | NM_020119.4 | c.2144G>A | p.Arg715His | missense_variant | 10/13 | ENST00000242351.10 | |
ZC3HAV1 | NM_001363491.2 | c.2510G>A | p.Arg837His | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3HAV1 | ENST00000242351.10 | c.2144G>A | p.Arg715His | missense_variant | 10/13 | 1 | NM_020119.4 | A2 | |
ZC3HAV1 | ENST00000464606.5 | c.2510G>A | p.Arg837His | missense_variant | 10/13 | 5 | P2 | ||
ZC3HAV1 | ENST00000680309.1 | c.1709G>A | p.Arg570His | missense_variant | 10/13 |
Frequencies
GnomAD3 genomes ? AF: 0.000309 AC: 47AN: 152230Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000143 AC: 36AN: 250888Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135578
GnomAD4 exome AF: 0.000123 AC: 180AN: 1460982Hom.: 1 Cov.: 30 AF XY: 0.000128 AC XY: 93AN XY: 726728
GnomAD4 genome ? AF: 0.000309 AC: 47AN: 152230Hom.: 0 Cov.: 33 AF XY: 0.000255 AC XY: 19AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.2144G>A (p.R715H) alteration is located in exon 10 (coding exon 10) of the ZC3HAV1 gene. This alteration results from a G to A substitution at nucleotide position 2144, causing the arginine (R) at amino acid position 715 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