chr19-53237000-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_182609.4(ZNF677):c.1727C>T(p.Thr576Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000598 in 1,571,480 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_182609.4 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 |
---|---|---|---|---|---|---|---|
ZNF677 | NM_182609.4 | c.1727C>T | p.Thr576Ile | missense_variant | 5/5 | ENST00000598513.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF677 | ENST00000598513.6 | c.1727C>T | p.Thr576Ile | missense_variant | 5/5 | 1 | NM_182609.4 | P1 | |
ZNF677 | ENST00000333952.8 | c.1727C>T | p.Thr576Ile | missense_variant | 3/3 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000316 AC: 48AN: 152056Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000131 AC: 28AN: 214426Hom.: 0 AF XY: 0.000104 AC XY: 12AN XY: 115446
GnomAD4 exome AF: 0.0000324 AC: 46AN: 1419308Hom.: 0 Cov.: 30 AF XY: 0.0000341 AC XY: 24AN XY: 703576
GnomAD4 genome ? AF: 0.000315 AC: 48AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.000296 AC XY: 22AN XY: 74384
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 16, 2021 | 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