chr6-20112995-G-A
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001080480.3(MBOAT1):c.1090C>T(p.Arg364Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,613,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic 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. R364L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001080480.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBOAT1 | NM_001080480.3 | c.1090C>T | p.Arg364Trp | missense_variant | 11/13 | ENST00000324607.8 | |
MBOAT1 | XM_006714999.3 | c.994C>T | p.Arg332Trp | missense_variant | 11/13 | ||
MBOAT1 | NR_073465.2 | n.1045C>T | non_coding_transcript_exon_variant | 8/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBOAT1 | ENST00000324607.8 | c.1090C>T | p.Arg364Trp | missense_variant | 11/13 | 1 | NM_001080480.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250640Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135436
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461434Hom.: 0 Cov.: 31 AF XY: 0.00000550 AC XY: 4AN XY: 727042
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152220Hom.: 0 Cov.: 31 AF XY: 0.0000538 AC XY: 4AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.1090C>T (p.R364W) alteration is located in exon 11 (coding exon 11) of the MBOAT1 gene. This alteration results from a C to T substitution at nucleotide position 1090, causing the arginine (R) at amino acid position 364 to be replaced by a tryptophan (W). 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