11-61906551-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_013401.4(RAB3IL1):c.572G>A(p.Arg191His) variant causes a missense change. The variant allele was found at a frequency of 0.0000171 in 1,580,742 control chromosomes in the GnomAD database, including 2 homozygotes. 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. R191C) 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 -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RAB3IL1 | ENST00000394836.7 | c.572G>A | p.Arg191His | missense_variant | Exon 5 of 10 | 1 | NM_013401.4 | ENSP00000378313.2 | ||
RAB3IL1 | ENST00000301773.9 | c.579+842G>A | intron_variant | Intron 4 of 8 | 1 | ENSP00000301773.5 | ||||
RAB3IL1 | ENST00000531922.2 | c.713G>A | p.Arg238His | missense_variant | Exon 5 of 11 | 3 | ENSP00000435444.2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000201 AC: 4AN: 198710Hom.: 0 AF XY: 0.00000934 AC XY: 1AN XY: 107054
GnomAD4 exome AF: 0.0000182 AC: 26AN: 1428664Hom.: 2 Cov.: 31 AF XY: 0.0000184 AC XY: 13AN XY: 707814
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152078Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74286
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.572G>A (p.R191H) 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 572, causing the arginine (R) at amino acid position 191 to be replaced by a histidine (H). 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