16-66925072-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_004165.3(RRAD):c.108C>A(p.His36Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000712 in 1,264,798 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004165.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RRAD | NM_004165.3 | c.108C>A | p.His36Gln | missense_variant | Exon 2 of 5 | ENST00000299759.11 | NP_004156.1 | |
RRAD | NM_001128850.2 | c.108C>A | p.His36Gln | missense_variant | Exon 2 of 5 | NP_001122322.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RRAD | ENST00000299759.11 | c.108C>A | p.His36Gln | missense_variant | Exon 2 of 5 | 1 | NM_004165.3 | ENSP00000299759.6 | ||
RRAD | ENST00000566577.1 | c.-121C>A | upstream_gene_variant | 5 | ENSP00000462559.1 | |||||
RRAD | ENST00000568915.5 | c.-100C>A | upstream_gene_variant | 5 | ENSP00000461995.1 |
Frequencies
GnomAD3 genomes AF: 0.0000461 AC: 7AN: 151956Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000180 AC: 2AN: 1112842Hom.: 0 Cov.: 30 AF XY: 0.00000188 AC XY: 1AN XY: 531782
GnomAD4 genome AF: 0.0000461 AC: 7AN: 151956Hom.: 0 Cov.: 33 AF XY: 0.0000674 AC XY: 5AN XY: 74230
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.108C>A (p.H36Q) alteration is located in exon 2 (coding exon 1) of the RRAD gene. This alteration results from a C to A substitution at nucleotide position 108, causing the histidine (H) at amino acid position 36 to be replaced by a glutamine (Q). 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