7-64077404-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001159522.3(ZNF727):c.355C>T(p.Arg119Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000438 in 1,551,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001159522.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF727 | NM_001159522.3 | c.355C>T | p.Arg119Cys | missense_variant | Exon 4 of 4 | ENST00000456806.3 | NP_001152994.1 | |
ZNF727 | XM_017012225.3 | c.259C>T | p.Arg87Cys | missense_variant | Exon 3 of 3 | XP_016867714.1 | ||
ZNF727 | XR_242241.4 | n.543C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | ||||
ZNF727 | XR_927469.2 | n.543C>T | non_coding_transcript_exon_variant | Exon 4 of 5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000190 AC: 3AN: 158024Hom.: 0 AF XY: 0.0000360 AC XY: 3AN XY: 83358
GnomAD4 exome AF: 0.0000457 AC: 64AN: 1399634Hom.: 0 Cov.: 55 AF XY: 0.0000420 AC XY: 29AN XY: 690300
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.355C>T (p.R119C) alteration is located in exon 4 (coding exon 4) of the ZNF727 gene. This alteration results from a C to T substitution at nucleotide position 355, causing the arginine (R) at amino acid position 119 to be replaced by a cysteine (C). 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