19-44892394-G-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001128917.2(TOMM40):āc.276G>Cā(p.Glu92Asp) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000155 in 1,613,878 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/22 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_001128917.2 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000782 AC: 119AN: 152096Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000207 AC: 52AN: 251482Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135912
GnomAD4 exome AF: 0.0000896 AC: 131AN: 1461664Hom.: 0 Cov.: 32 AF XY: 0.0000784 AC XY: 57AN XY: 727126
GnomAD4 genome AF: 0.000782 AC: 119AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.000658 AC XY: 49AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Apr 04, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at