19-54174100-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBS1_Supporting
The NM_024298.5(MBOAT7):c.1363C>T(p.Arg455Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000023 in 1,606,276 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R455Q) has been classified as Likely benign.
Frequency
Consequence
NM_024298.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152008Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000374 AC: 9AN: 240794Hom.: 0 AF XY: 0.0000305 AC XY: 4AN XY: 131088
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1454268Hom.: 0 Cov.: 31 AF XY: 0.0000152 AC XY: 11AN XY: 723482
GnomAD4 genome AF: 0.000105 AC: 16AN: 152008Hom.: 0 Cov.: 32 AF XY: 0.0000942 AC XY: 7AN XY: 74276
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 10, 2022 | The c.1363C>T (p.R455W) alteration is located in exon 8 (coding exon 7) of the MBOAT7 gene. This alteration results from a C to T substitution at nucleotide position 1363, causing the arginine (R) at amino acid position 455 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