19-54174097-T-C
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_024298.5(MBOAT7):āc.1366A>Gā(p.Lys456Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,607,138 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 (ā ā ).
Frequency
Consequence
NM_024298.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MBOAT7 | NM_024298.5 | c.1366A>G | p.Lys456Glu | missense_variant | 8/8 | ENST00000245615.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MBOAT7 | ENST00000245615.6 | c.1366A>G | p.Lys456Glu | missense_variant | 8/8 | 1 | NM_024298.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 151960Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000495 AC: 12AN: 242356Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131848
GnomAD4 exome AF: 0.00000893 AC: 13AN: 1455178Hom.: 0 Cov.: 31 AF XY: 0.00000276 AC XY: 2AN XY: 723904
GnomAD4 genome AF: 0.0000395 AC: 6AN: 151960Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74224
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2021 | The c.1366A>G (p.K456E) alteration is located in exon 8 (coding exon 7) of the MBOAT7 gene. This alteration results from a A to G substitution at nucleotide position 1366, causing the lysine (K) at amino acid position 456 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Intellectual disability, autosomal recessive 57 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 06, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at