X-153346830-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001367757.1(ZNF275):c.145G>A(p.Ala49Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000503 in 1,191,956 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 21 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A49V) has been classified as Likely benign.
Frequency
Consequence
NM_001367757.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZNF275 | NM_001367757.1 | c.145G>A | p.Ala49Thr | missense_variant | 4/4 | ENST00000650114.2 | |
ZNF275 | NM_001080485.4 | c.145G>A | p.Ala49Thr | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZNF275 | ENST00000650114.2 | c.145G>A | p.Ala49Thr | missense_variant | 4/4 | NM_001367757.1 | A2 | ||
ZNF275 | ENST00000370249.3 | c.-15G>A | 5_prime_UTR_variant | 3/3 | 1 | P2 | |||
ZNF275 | ENST00000370251.3 | c.145G>A | p.Ala49Thr | missense_variant | 4/5 | 2 | |||
ZNF275 | ENST00000647705.1 | n.1357G>A | non_coding_transcript_exon_variant | 2/2 |
Frequencies
GnomAD3 genomes AF: 0.000206 AC: 23AN: 111784Hom.: 0 Cov.: 23 AF XY: 0.000265 AC XY: 9AN XY: 33968
GnomAD3 exomes AF: 0.0000733 AC: 12AN: 163641Hom.: 0 AF XY: 0.0000185 AC XY: 1AN XY: 54085
GnomAD4 exome AF: 0.0000333 AC: 36AN: 1080120Hom.: 0 Cov.: 31 AF XY: 0.0000313 AC XY: 11AN XY: 351632
GnomAD4 genome AF: 0.000215 AC: 24AN: 111836Hom.: 0 Cov.: 23 AF XY: 0.000294 AC XY: 10AN XY: 34030
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 19, 2022 | The c.145G>A (p.A49T) alteration is located in exon 4 (coding exon 3) of the ZNF275 gene. This alteration results from a G to A substitution at nucleotide position 145, causing the alanine (A) at amino acid position 49 to be replaced by a threonine (T). 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