20-37301412-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001003897.2(MANBAL):c.149C>T(p.Ala50Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,610,476 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001003897.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000644 AC: 98AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000184 AC: 46AN: 249518Hom.: 0 AF XY: 0.000156 AC XY: 21AN XY: 134914
GnomAD4 exome AF: 0.0000857 AC: 125AN: 1458206Hom.: 0 Cov.: 30 AF XY: 0.0000744 AC XY: 54AN XY: 725506
GnomAD4 genome AF: 0.000644 AC: 98AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000645 AC XY: 48AN XY: 74458
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.149C>T (p.A50V) alteration is located in exon 3 (coding exon 1) of the MANBAL gene. This alteration results from a C to T substitution at nucleotide position 149, causing the alanine (A) at amino acid position 50 to be replaced by a valine (V). 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