6-20112888-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001080480.3(MBOAT1):c.1197A>C(p.Leu399Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,720 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_001080480.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBOAT1 | NM_001080480.3 | c.1197A>C | p.Leu399Phe | missense_variant | 11/13 | ENST00000324607.8 | |
MBOAT1 | XM_006714999.3 | c.1101A>C | p.Leu367Phe | missense_variant | 11/13 | ||
MBOAT1 | NR_073465.2 | n.1152A>C | non_coding_transcript_exon_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBOAT1 | ENST00000324607.8 | c.1197A>C | p.Leu399Phe | missense_variant | 11/13 | 1 | NM_001080480.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152164Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250856Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135574
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461556Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727106
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152164Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 12, 2024 | The c.1197A>C (p.L399F) alteration is located in exon 11 (coding exon 11) of the MBOAT1 gene. This alteration results from a A to C substitution at nucleotide position 1197, causing the leucine (L) at amino acid position 399 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