21-32311800-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001379228.1(MRAP):c.323C>T(p.Ala108Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,614,062 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. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A108T) has been classified as Uncertain significance.
Frequency
Consequence
NM_001379228.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MRAP | ENST00000303645.10 | c.323C>T | p.Ala108Val | missense_variant | Exon 3 of 3 | 1 | NM_001379228.1 | ENSP00000306697.5 | ||
URB1 | ENST00000382751 | c.*3118G>A | 3_prime_UTR_variant | Exon 39 of 39 | 1 | NM_014825.3 | ENSP00000372199.3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249640Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135110
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461764Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727198
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152298Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74452
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.323C>T (p.A108V) alteration is located in exon 5 (coding exon 3) of the MRAP gene. This alteration results from a C to T substitution at nucleotide position 323, causing the alanine (A) at amino acid position 108 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