chr6-20109674-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001080480.3(MBOAT1):c.1285G>A(p.Val429Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,614,140 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001080480.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MBOAT1 | NM_001080480.3 | c.1285G>A | p.Val429Ile | missense_variant | Exon 12 of 13 | ENST00000324607.8 | NP_001073949.1 | |
MBOAT1 | XM_006714999.3 | c.1189G>A | p.Val397Ile | missense_variant | Exon 12 of 13 | XP_006715062.1 | ||
MBOAT1 | NR_073465.2 | n.1240G>A | non_coding_transcript_exon_variant | Exon 9 of 10 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251434Hom.: 0 AF XY: 0.000110 AC XY: 15AN XY: 135876
GnomAD4 exome AF: 0.0000547 AC: 80AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.0000523 AC XY: 38AN XY: 727232
GnomAD4 genome AF: 0.000144 AC: 22AN: 152276Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at