22-19433328-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001318151.2(MRPL40):c.-16C>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000962 in 1,611,498 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001318151.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MRPL40 | NM_003776.4 | c.117C>G | p.Phe39Leu | missense_variant | Exon 2 of 4 | ENST00000333130.4 | NP_003767.2 | |
MRPL40 | NM_001318151.2 | c.-16C>G | 5_prime_UTR_premature_start_codon_gain_variant | Exon 2 of 4 | NP_001305080.1 | |||
MRPL40 | NM_001318151.2 | c.-16C>G | 5_prime_UTR_variant | Exon 2 of 4 | NP_001305080.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000499 AC: 76AN: 152188Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000111 AC: 28AN: 251370Hom.: 0 AF XY: 0.0000662 AC XY: 9AN XY: 135884
GnomAD4 exome AF: 0.0000541 AC: 79AN: 1459192Hom.: 0 Cov.: 28 AF XY: 0.0000441 AC XY: 32AN XY: 726064
GnomAD4 genome AF: 0.000499 AC: 76AN: 152306Hom.: 0 Cov.: 33 AF XY: 0.000457 AC XY: 34AN XY: 74476
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.117C>G (p.F39L) alteration is located in exon 2 (coding exon 2) of the MRPL40 gene. This alteration results from a C to G substitution at nucleotide position 117, causing the phenylalanine (F) at amino acid position 39 to be replaced by a leucine (L). 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