7-64068892-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001159522.3(ZNF727):c.5G>A(p.Arg2Gln) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000754 in 1,592,138 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001159522.3 missense, splice_region
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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF727 | NM_001159522.3 | c.5G>A | p.Arg2Gln | missense_variant, splice_region_variant | 2/4 | ENST00000456806.3 | NP_001152994.1 | |
ZNF727 | XM_017012225.3 | c.5G>A | p.Arg2Gln | missense_variant, splice_region_variant | 2/3 | XP_016867714.1 | ||
ZNF727 | XR_242241.4 | n.193G>A | splice_region_variant, non_coding_transcript_exon_variant | 2/5 | ||||
ZNF727 | XR_927469.2 | n.193G>A | splice_region_variant, non_coding_transcript_exon_variant | 2/5 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151986Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000908 AC: 2AN: 220166Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 119102
GnomAD4 exome AF: 0.00000764 AC: 11AN: 1440152Hom.: 0 Cov.: 31 AF XY: 0.00000280 AC XY: 2AN XY: 714848
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151986Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74218
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2023 | The c.5G>A (p.R2Q) alteration is located in exon 2 (coding exon 2) of the ZNF727 gene. This alteration results from a G to A substitution at nucleotide position 5, causing the arginine (R) at amino acid position 2 to be replaced by a glutamine (Q). 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