chr7-130018692-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_016478.5(ZC3HC1):c.1481G>A(p.Arg494Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000242 in 1,612,084 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016478.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZC3HC1 | ENST00000358303.9 | c.1481G>A | p.Arg494Gln | missense_variant | Exon 10 of 10 | 1 | NM_016478.5 | ENSP00000351052.4 | ||
ZC3HC1 | ENST00000481503.5 | c.1352G>A | p.Arg451Gln | missense_variant | Exon 10 of 10 | 5 | ENSP00000418533.1 | |||
ZC3HC1 | ENST00000467642.5 | n.*1365G>A | non_coding_transcript_exon_variant | Exon 11 of 11 | 2 | ENSP00000419509.1 | ||||
ZC3HC1 | ENST00000648450.1 | n.*1491G>A | non_coding_transcript_exon_variant | Exon 12 of 12 | ENSP00000498166.1 | |||||
ZC3HC1 | ENST00000467642.5 | n.*1365G>A | 3_prime_UTR_variant | Exon 11 of 11 | 2 | ENSP00000419509.1 | ||||
ZC3HC1 | ENST00000648450.1 | n.*1491G>A | 3_prime_UTR_variant | Exon 12 of 12 | ENSP00000498166.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251134Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135718
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460032Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 726026
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74274
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1481G>A (p.R494Q) alteration is located in exon 10 (coding exon 10) of the ZC3HC1 gene. This alteration results from a G to A substitution at nucleotide position 1481, causing the arginine (R) at amino acid position 494 to be replaced by a glutamine (Q). 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