11-96341439-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032427.4(MAML2):c.457G>A(p.Glu153Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000779 in 1,549,898 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032427.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAML2 | NM_032427.4 | c.457G>A | p.Glu153Lys | missense_variant | Exon 1 of 5 | ENST00000524717.6 | NP_115803.1 | |
MIR1260B | NR_036125.1 | n.2C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | ||||
MIR1260B | unassigned_transcript_1951 | n.-8C>T | upstream_gene_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000232 AC: 35AN: 150994Hom.: 0 AF XY: 0.000225 AC XY: 18AN XY: 80028
GnomAD4 exome AF: 0.000830 AC: 1160AN: 1397580Hom.: 2 Cov.: 32 AF XY: 0.000778 AC XY: 536AN XY: 689018
GnomAD4 genome AF: 0.000309 AC: 47AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000295 AC XY: 22AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.457G>A (p.E153K) alteration is located in exon 1 (coding exon 1) of the MAML2 gene. This alteration results from a G to A substitution at nucleotide position 457, causing the glutamic acid (E) at amino acid position 153 to be replaced by a lysine (K). 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