chrX-46500597-ATG-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS2
The NM_001190417.2(ZNF674):c.975_976delCA(p.Ile326fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000504 in 1,209,643 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001190417.2 frameshift
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.975_976delCA | p.Ile326fs | frameshift_variant | Exon 6 of 6 | ENST00000683375.1 | NP_001177346.1 | |
ZNF674 | NM_001039891.3 | c.990_991delCA | p.Ile331fs | frameshift_variant | Exon 6 of 6 | NP_001034980.1 | ||
ZNF674 | NM_001146291.2 | c.972_973delCA | p.Ile325fs | frameshift_variant | Exon 6 of 6 | NP_001139763.1 | ||
ZNF674 | XM_011543943.4 | c.987_988delCA | p.Ile330fs | frameshift_variant | Exon 6 of 6 | XP_011542245.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ZNF674 | ENST00000683375.1 | c.975_976delCA | p.Ile326fs | frameshift_variant | Exon 6 of 6 | NM_001190417.2 | ENSP00000506769.1 | |||
ZNF674 | ENST00000523374.5 | c.990_991delCA | p.Ile331fs | frameshift_variant | Exon 6 of 6 | 1 | ENSP00000429148.1 | |||
ZNF674 | ENST00000414387.6 | c.972_973delCA | p.Ile325fs | frameshift_variant | Exon 5 of 5 | 3 | ENSP00000428248.1 |
Frequencies
GnomAD3 genomes AF: 0.0000804 AC: 9AN: 112004Hom.: 0 Cov.: 22 AF XY: 0.0000877 AC XY: 3AN XY: 34226
GnomAD3 exomes AF: 0.0000331 AC: 6AN: 181530Hom.: 0 AF XY: 0.0000594 AC XY: 4AN XY: 67312
GnomAD4 exome AF: 0.0000474 AC: 52AN: 1097639Hom.: 0 AF XY: 0.0000441 AC XY: 16AN XY: 363087
GnomAD4 genome AF: 0.0000804 AC: 9AN: 112004Hom.: 0 Cov.: 22 AF XY: 0.0000877 AC XY: 3AN XY: 34226
ClinVar
Submissions by phenotype
not provided Uncertain:1
- -
not specified Benign:1
p.Ile331X (c.990_9901del) in exon 6 of ZNF674: This variant is not expected to h ave clinical significance because it has been identified in 0.4% (26/6239) of Eu ropean chromosomes by the NHLBI Exome Sequence Project (http://evs.gs.washington .edu/EVS). This variant is predicted to cause a frameshift, which alters the pro tein?s amino acid sequence beginning at position 331 and leads to an immediate p remature termination codon. This alteration occurs within the last exon and is m ore likely to escape nonsense mediated decay (NMD) and result in a truncated pro tein. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at