chr1-90937700-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_201269.3(ZNF644):c.3473C>A(p.Pro1158Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,692 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_201269.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF644 | NM_201269.3 | c.3473C>A | p.Pro1158Gln | missense_variant | 4/6 | ENST00000337393.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF644 | ENST00000337393.10 | c.3473C>A | p.Pro1158Gln | missense_variant | 4/6 | 1 | NM_201269.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250852Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135554
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461684Hom.: 0 Cov.: 33 AF XY: 0.0000193 AC XY: 14AN XY: 727140
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74256
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 16, 2022 | The c.3473C>A (p.P1158Q) alteration is located in exon 4 (coding exon 3) of the ZNF644 gene. This alteration results from a C to A substitution at nucleotide position 3473, causing the proline (P) at amino acid position 1158 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