4-139890297-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_018717.5(MAML3):c.1139C>T(p.Ser380Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000726 in 1,613,834 control chromosomes in the GnomAD database, including 1 homozygotes. 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.1139C>T | p.Ser380Phe | missense_variant | Exon 2 of 5 | ENST00000509479.6 | NP_061187.3 | |
MAML3 | XM_047415929.1 | c.1139C>T | p.Ser380Phe | missense_variant | Exon 2 of 5 | XP_047271885.1 | ||
MAML3 | XM_047415930.1 | c.1139C>T | p.Ser380Phe | missense_variant | Exon 2 of 3 | XP_047271886.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000375 AC: 57AN: 152174Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000386 AC: 96AN: 248628Hom.: 0 AF XY: 0.000297 AC XY: 40AN XY: 134876
GnomAD4 exome AF: 0.000762 AC: 1114AN: 1461542Hom.: 1 Cov.: 35 AF XY: 0.000685 AC XY: 498AN XY: 727046
GnomAD4 genome AF: 0.000374 AC: 57AN: 152292Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1139C>T (p.S380F) alteration is located in exon 2 (coding exon 2) of the MAML3 gene. This alteration results from a C to T substitution at nucleotide position 1139, causing the serine (S) at amino acid position 380 to be replaced by a phenylalanine (F). 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