X-46500265-C-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001190417.2(ZNF674):c.1309G>T(p.Glu437*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000628 in 1,209,720 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 14 hemizygotes in GnomAD. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_001190417.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZNF674 | NM_001190417.2 | c.1309G>T | p.Glu437* | stop_gained | Exon 6 of 6 | ENST00000683375.1 | NP_001177346.1 | |
ZNF674 | NM_001039891.3 | c.1324G>T | p.Glu442* | stop_gained | Exon 6 of 6 | NP_001034980.1 | ||
ZNF674 | NM_001146291.2 | c.1306G>T | p.Glu436* | stop_gained | Exon 6 of 6 | NP_001139763.1 | ||
ZNF674 | XM_011543943.4 | c.1321G>T | p.Glu441* | stop_gained | Exon 6 of 6 | XP_011542245.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF674 | ENST00000683375.1 | c.1309G>T | p.Glu437* | stop_gained | Exon 6 of 6 | NM_001190417.2 | ENSP00000506769.1 | |||
ZNF674 | ENST00000523374.5 | c.1324G>T | p.Glu442* | stop_gained | Exon 6 of 6 | 1 | ENSP00000429148.1 | |||
ZNF674 | ENST00000414387.6 | c.1306G>T | p.Glu436* | stop_gained | Exon 5 of 5 | 3 | ENSP00000428248.1 |
Frequencies
GnomAD3 genomes AF: 0.000340 AC: 38AN: 111825Hom.: 0 Cov.: 23 AF XY: 0.000206 AC XY: 7AN XY: 34023
GnomAD3 exomes AF: 0.0000826 AC: 15AN: 181584Hom.: 0 AF XY: 0.0000297 AC XY: 2AN XY: 67236
GnomAD4 exome AF: 0.0000346 AC: 38AN: 1097841Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 7AN XY: 363229
GnomAD4 genome AF: 0.000340 AC: 38AN: 111879Hom.: 0 Cov.: 23 AF XY: 0.000205 AC XY: 7AN XY: 34087
ClinVar
Submissions by phenotype
ZNF674-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