chrX-153346831-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001367757.1(ZNF275):c.146C>T(p.Ala49Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000252 in 1,192,450 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A49T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001367757.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF275 | NM_001367757.1 | c.146C>T | p.Ala49Val | missense_variant | 4/4 | ENST00000650114.2 | |
ZNF275 | NM_001080485.4 | c.146C>T | p.Ala49Val | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF275 | ENST00000650114.2 | c.146C>T | p.Ala49Val | missense_variant | 4/4 | NM_001367757.1 | A2 | ||
ZNF275 | ENST00000370249.3 | c.-14C>T | 5_prime_UTR_variant | 3/3 | 1 | P2 | |||
ZNF275 | ENST00000370251.3 | c.146C>T | p.Ala49Val | missense_variant | 4/5 | 2 | |||
ZNF275 | ENST00000647705.1 | n.1358C>T | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111886Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34056
GnomAD3 exomes AF: 0.0000122 AC: 2AN: 163930Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 54288
GnomAD4 exome AF: 0.0000259 AC: 28AN: 1080564Hom.: 0 Cov.: 31 AF XY: 0.0000313 AC XY: 11AN XY: 351924
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111886Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34056
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at