chr4-76082208-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001130016.3(ART3):c.454C>A(p.Pro152Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000446 in 1,614,136 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001130016.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ART3 | NM_001130016.3 | c.454C>A | p.Pro152Thr | missense_variant | 3/12 | ENST00000355810.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ART3 | ENST00000355810.9 | c.454C>A | p.Pro152Thr | missense_variant | 3/12 | 1 | NM_001130016.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.000217 AC: 33AN: 152132Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251428Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135896
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461886Hom.: 0 Cov.: 32 AF XY: 0.0000289 AC XY: 21AN XY: 727242
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152250Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 07, 2023 | The c.454C>A (p.P152T) alteration is located in exon 3 (coding exon 2) of the ART3 gene. This alteration results from a C to A substitution at nucleotide position 454, causing the proline (P) at amino acid position 152 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