19-11487132-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_138783.4(ZNF653):āc.1198A>Gā(p.Lys400Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,612,314 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_138783.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF653 | NM_138783.4 | c.1198A>G | p.Lys400Glu | missense_variant | 5/9 | ENST00000293771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF653 | ENST00000293771.10 | c.1198A>G | p.Lys400Glu | missense_variant | 5/9 | 1 | NM_138783.4 | P1 | |
ZNF653 | ENST00000592756.1 | c.34A>G | p.Lys12Glu | missense_variant | 2/5 | 3 | |||
ZNF653 | ENST00000590548.5 | n.1366A>G | non_coding_transcript_exon_variant | 4/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 250054Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135332
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1460074Hom.: 1 Cov.: 33 AF XY: 0.0000413 AC XY: 30AN XY: 726424
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 20, 2023 | The c.1198A>G (p.K400E) alteration is located in exon 5 (coding exon 5) of the ZNF653 gene. This alteration results from a A to G substitution at nucleotide position 1198, causing the lysine (K) at amino acid position 400 to be replaced by a glutamic acid (E). 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