4-139890232-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000509479.6(MAML3):c.1204G>A(p.Ala402Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,613,340 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000509479.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAML3 | NM_018717.5 | c.1204G>A | p.Ala402Thr | missense_variant | 2/5 | ENST00000509479.6 | NP_061187.3 | |
MAML3 | XM_047415929.1 | c.1204G>A | p.Ala402Thr | missense_variant | 2/5 | XP_047271885.1 | ||
MAML3 | XM_047415930.1 | c.1204G>A | p.Ala402Thr | missense_variant | 2/3 | XP_047271886.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MAML3 | ENST00000509479.6 | c.1204G>A | p.Ala402Thr | missense_variant | 2/5 | 1 | NM_018717.5 | ENSP00000421180 | P1 | |
MAML3 | ENST00000502696.1 | c.111-159565G>A | intron_variant | 2 | ENSP00000422783 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 248622Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134838
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1461322Hom.: 0 Cov.: 35 AF XY: 0.0000165 AC XY: 12AN XY: 726900
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74248
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2023 | The c.1204G>A (p.A402T) alteration is located in exon 2 (coding exon 2) of the MAML3 gene. This alteration results from a G to A substitution at nucleotide position 1204, causing the alanine (A) at amino acid position 402 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