rs12117237
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_201269.3(ZNF644):c.2119A>G(p.Lys707Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00412 in 1,614,010 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_201269.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF644 | NM_201269.3 | c.2119A>G | p.Lys707Glu | missense_variant | 3/6 | ENST00000337393.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF644 | ENST00000337393.10 | c.2119A>G | p.Lys707Glu | missense_variant | 3/6 | 1 | NM_201269.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00323 AC: 491AN: 152122Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00364 AC: 912AN: 250860Hom.: 2 AF XY: 0.00375 AC XY: 509AN XY: 135734
GnomAD4 exome AF: 0.00421 AC: 6157AN: 1461770Hom.: 20 Cov.: 34 AF XY: 0.00419 AC XY: 3048AN XY: 727180
GnomAD4 genome ? AF: 0.00323 AC: 492AN: 152240Hom.: 1 Cov.: 32 AF XY: 0.00359 AC XY: 267AN XY: 74450
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | May 16, 2018 | - - |
ZNF644-related condition Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 12, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at