15-84783143-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_014630.3(ZNF592):c.468C>T(p.Asn156Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,614,048 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_014630.3 synonymous
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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF592 | NM_014630.3 | c.468C>T | p.Asn156Asn | synonymous_variant | Exon 4 of 11 | ENST00000560079.7 | NP_055445.2 | |
ZNF592 | XM_005254996.4 | c.468C>T | p.Asn156Asn | synonymous_variant | Exon 3 of 10 | XP_005255053.1 | ||
ZNF592 | XM_011522246.3 | c.468C>T | p.Asn156Asn | synonymous_variant | Exon 4 of 11 | XP_011520548.1 | ||
ZNF592 | XM_011522247.3 | c.468C>T | p.Asn156Asn | synonymous_variant | Exon 3 of 10 | XP_011520549.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF592 | ENST00000560079.7 | c.468C>T | p.Asn156Asn | synonymous_variant | Exon 4 of 11 | 1 | NM_014630.3 | ENSP00000452877.2 | ||
ZNF592 | ENST00000559607.1 | n.468C>T | non_coding_transcript_exon_variant | Exon 2 of 9 | 1 | ENSP00000453491.1 | ||||
ZNF592 | ENST00000299927.4 | c.468C>T | p.Asn156Asn | synonymous_variant | Exon 1 of 8 | 2 | ENSP00000299927.3 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251018Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135752
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461850Hom.: 0 Cov.: 32 AF XY: 0.0000165 AC XY: 12AN XY: 727222
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152198Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74348
ClinVar
Submissions by phenotype
ZNF592-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at