X-48060492-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001282201.2(ZNF630):c.196C>A(p.Pro66Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000357 in 1,204,623 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001282201.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF630 | NM_001282201.2 | c.196C>A | p.Pro66Thr | missense_variant | 4/5 | ENST00000276054.9 | NP_001269130.1 | |
ZNF630-AS1 | NR_046742.2 | n.123+4060G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF630 | ENST00000276054.9 | c.196C>A | p.Pro66Thr | missense_variant | 4/5 | 1 | NM_001282201.2 | ENSP00000354683 | P1 | |
ZNF630-AS1 | ENST00000614448.1 | n.123+4060G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000633 AC: 7AN: 110612Hom.: 0 Cov.: 22 AF XY: 0.0000909 AC XY: 3AN XY: 32998
GnomAD3 exomes AF: 0.000117 AC: 21AN: 178745Hom.: 0 AF XY: 0.0000766 AC XY: 5AN XY: 65239
GnomAD4 exome AF: 0.0000329 AC: 36AN: 1094011Hom.: 0 Cov.: 30 AF XY: 0.0000250 AC XY: 9AN XY: 359621
GnomAD4 genome AF: 0.0000633 AC: 7AN: 110612Hom.: 0 Cov.: 22 AF XY: 0.0000909 AC XY: 3AN XY: 32998
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 10, 2021 | The c.196C>A (p.P66T) alteration is located in exon 4 (coding exon 3) of the ZNF630 gene. This alteration results from a C to A substitution at nucleotide position 196, causing the proline (P) at amino acid position 66 to be replaced by a threonine (T). 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