4-139890672-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_018717.5(MAML3):c.764C>A(p.Pro255His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000103 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018717.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAML3 | NM_018717.5 | c.764C>A | p.Pro255His | missense_variant | Exon 2 of 5 | ENST00000509479.6 | NP_061187.3 | |
MAML3 | XM_047415929.1 | c.764C>A | p.Pro255His | missense_variant | Exon 2 of 5 | XP_047271885.1 | ||
MAML3 | XM_047415930.1 | c.764C>A | p.Pro255His | missense_variant | Exon 2 of 3 | XP_047271886.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000789 AC: 12AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000321 AC: 8AN: 249276Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135228
GnomAD4 exome AF: 0.000105 AC: 154AN: 1461672Hom.: 0 Cov.: 35 AF XY: 0.000106 AC XY: 77AN XY: 727116
GnomAD4 genome AF: 0.0000789 AC: 12AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.764C>A (p.P255H) alteration is located in exon 2 (coding exon 2) of the MAML3 gene. This alteration results from a C to A substitution at nucleotide position 764, causing the proline (P) at amino acid position 255 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