11-61906519-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013401.4(RAB3IL1):c.604G>A(p.Ala202Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000617 in 1,555,814 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A202S) has been classified as Uncertain significance.
Frequency
Consequence
NM_013401.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB3IL1 | ENST00000394836.7 | c.604G>A | p.Ala202Thr | missense_variant | Exon 5 of 10 | 1 | NM_013401.4 | ENSP00000378313.2 | ||
RAB3IL1 | ENST00000301773.9 | c.579+874G>A | intron_variant | Intron 4 of 8 | 1 | ENSP00000301773.5 | ||||
RAB3IL1 | ENST00000531922.2 | c.745G>A | p.Ala249Thr | missense_variant | Exon 5 of 11 | 3 | ENSP00000435444.2 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152002Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000424 AC: 7AN: 164926Hom.: 0 AF XY: 0.0000569 AC XY: 5AN XY: 87842
GnomAD4 exome AF: 0.0000620 AC: 87AN: 1403812Hom.: 0 Cov.: 31 AF XY: 0.0000721 AC XY: 50AN XY: 693450
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74236
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.604G>A (p.A202T) alteration is located in exon 5 (coding exon 5) of the RAB3IL1 gene. This alteration results from a G to A substitution at nucleotide position 604, causing the alanine (A) at amino acid position 202 to be replaced by a threonine (T). 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