6-63578977-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003463.5(PTP4A1):c.278G>A(p.Arg93His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000933 in 1,607,604 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 (★).
Frequency
Consequence
NM_003463.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PTP4A1 | NM_003463.5 | c.278G>A | p.Arg93His | missense_variant | Exon 4 of 6 | ENST00000626021.3 | NP_003454.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152106Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000242 AC: 6AN: 248146Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134316
GnomAD4 exome AF: 0.00000618 AC: 9AN: 1455498Hom.: 0 Cov.: 31 AF XY: 0.00000691 AC XY: 5AN XY: 724066
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152106Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.278G>A (p.R93H) alteration is located in exon 4 (coding exon 3) of the PTP4A1 gene. This alteration results from a G to A substitution at nucleotide position 278, causing the arginine (R) at amino acid position 93 to be replaced by a histidine (H). 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