chr7-139055275-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_020119.4(ZC3HAV1):c.2117C>T(p.Ser706Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000744 in 1,612,952 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Synonymous variant affecting the same amino acid position (i.e. S706S) has been classified as Benign.
Frequency
Consequence
NM_020119.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
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.2117C>T | p.Ser706Leu | missense_variant | 10/13 | ENST00000242351.10 | |
ZC3HAV1 | NM_001363491.2 | c.2483C>T | p.Ser828Leu | missense_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZC3HAV1 | ENST00000242351.10 | c.2117C>T | p.Ser706Leu | missense_variant | 10/13 | 1 | NM_020119.4 | A2 | |
ZC3HAV1 | ENST00000464606.5 | c.2483C>T | p.Ser828Leu | missense_variant | 10/13 | 5 | P2 | ||
ZC3HAV1 | ENST00000680309.1 | c.1682C>T | p.Ser561Leu | missense_variant | 10/13 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 250812Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135540
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1460724Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 726572
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 06, 2023 | The c.2117C>T (p.S706L) alteration is located in exon 10 (coding exon 10) of the ZC3HAV1 gene. This alteration results from a C to T substitution at nucleotide position 2117, causing the serine (S) at amino acid position 706 to be replaced by a leucine (L). 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