NM_080879.3:c.199C>A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_080879.3(RAB40A):c.199C>A(p.Leu67Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,209,405 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_080879.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000899 AC: 1AN: 111187Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33375
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183369Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67809
GnomAD4 exome AF: 0.00000182 AC: 2AN: 1098218Hom.: 0 Cov.: 33 AF XY: 0.00000275 AC XY: 1AN XY: 363572
GnomAD4 genome AF: 0.00000899 AC: 1AN: 111187Hom.: 0 Cov.: 22 AF XY: 0.0000300 AC XY: 1AN XY: 33375
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.199C>A (p.L67I) alteration is located in exon 3 (coding exon 1) of the RAB40A gene. This alteration results from a C to A substitution at nucleotide position 199, causing the leucine (L) at amino acid position 67 to be replaced by an isoleucine (I). 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