19-11487592-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_138783.4(ZNF653):c.871G>A(p.Ala291Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000923 in 1,613,774 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 Likely benign (★).
Frequency
Consequence
NM_138783.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF653 | NM_138783.4 | c.871G>A | p.Ala291Thr | missense_variant | 4/9 | ENST00000293771.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF653 | ENST00000293771.10 | c.871G>A | p.Ala291Thr | missense_variant | 4/9 | 1 | NM_138783.4 | P1 | |
ZNF653 | ENST00000590548.5 | n.906G>A | non_coding_transcript_exon_variant | 4/8 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152242Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250160Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135520
GnomAD4 exome AF: 0.0000944 AC: 138AN: 1461532Hom.: 0 Cov.: 33 AF XY: 0.0000949 AC XY: 69AN XY: 727116
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74382
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 24, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at