chr6-143765581-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001100164.2(PHACTR2):c.1015C>G(p.Pro339Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,614,040 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001100164.2 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 |
---|---|---|---|---|---|---|---|
PHACTR2 | NM_001100164.2 | c.1015C>G | p.Pro339Ala | missense_variant | 6/13 | ENST00000440869.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PHACTR2 | ENST00000440869.7 | c.1015C>G | p.Pro339Ala | missense_variant | 6/13 | 2 | NM_001100164.2 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249268Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135242
GnomAD4 exome AF: 0.0000383 AC: 56AN: 1461726Hom.: 1 Cov.: 33 AF XY: 0.0000385 AC XY: 28AN XY: 727172
GnomAD4 genome ? AF: 0.0000525 AC: 8AN: 152314Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2024 | The c.1015C>G (p.P339A) alteration is located in exon 6 (coding exon 6) of the PHACTR2 gene. This alteration results from a C to G substitution at nucleotide position 1015, causing the proline (P) at amino acid position 339 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