NM_002431.4:c.634C>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002431.4(MNAT1):c.634C>T(p.Leu212Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000992 in 1,612,754 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_002431.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MNAT1 | NM_002431.4 | c.634C>T | p.Leu212Phe | missense_variant | Exon 6 of 8 | ENST00000261245.9 | NP_002422.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250974Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135660
GnomAD4 exome AF: 0.00000548 AC: 8AN: 1460696Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 726670
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74258
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.634C>T (p.L212F) alteration is located in exon 6 (coding exon 6) of the MNAT1 gene. This alteration results from a C to T substitution at nucleotide position 634, causing the leucine (L) at amino acid position 212 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