chr1-28473598-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001048183.3(PHACTR4):āc.868C>Gā(p.Pro290Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000279 in 1,613,740 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P290L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001048183.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PHACTR4 | NM_001048183.3 | c.868C>G | p.Pro290Ala | missense_variant | 7/14 | ENST00000373839.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHACTR4 | ENST00000373839.8 | c.868C>G | p.Pro290Ala | missense_variant | 7/14 | 1 | NM_001048183.3 | P2 | |
PHACTR4 | ENST00000493669.2 | c.*704C>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/17 | 1 | ||||
PHACTR4 | ENST00000373836.4 | c.898C>G | p.Pro300Ala | missense_variant | 6/13 | 5 | A2 | ||
PHACTR4 | ENST00000632421.1 | c.*858C>G | 3_prime_UTR_variant, NMD_transcript_variant | 8/15 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152126Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249130Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135140
GnomAD4 exome AF: 0.0000157 AC: 23AN: 1461496Hom.: 0 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 727042
GnomAD4 genome AF: 0.000145 AC: 22AN: 152244Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.898C>G (p.P300A) alteration is located in exon 6 (coding exon 6) of the PHACTR4 gene. This alteration results from a C to G substitution at nucleotide position 898, causing the proline (P) at amino acid position 300 to be replaced by an alanine (A). 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