16-66925016-G-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000299759.11(RRAD):c.164C>A(p.Ala55Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000439 in 1,413,522 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 (★).
Frequency
Consequence
ENST00000299759.11 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RRAD | NM_004165.3 | c.164C>A | p.Ala55Asp | missense_variant | 2/5 | ENST00000299759.11 | NP_004156.1 | |
RRAD | NM_001128850.2 | c.164C>A | p.Ala55Asp | missense_variant | 2/5 | NP_001122322.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RRAD | ENST00000299759.11 | c.164C>A | p.Ala55Asp | missense_variant | 2/5 | 1 | NM_004165.3 | ENSP00000299759 | P1 | |
RRAD | ENST00000568915.5 | upstream_gene_variant | 5 | ENSP00000461995 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152058Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000500 AC: 4AN: 80020Hom.: 0 AF XY: 0.0000432 AC XY: 2AN XY: 46276
GnomAD4 exome AF: 0.0000325 AC: 41AN: 1261464Hom.: 0 Cov.: 30 AF XY: 0.0000307 AC XY: 19AN XY: 619324
GnomAD4 genome AF: 0.000138 AC: 21AN: 152058Hom.: 0 Cov.: 33 AF XY: 0.000162 AC XY: 12AN XY: 74280
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 17, 2022 | The c.164C>A (p.A55D) 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 164, causing the alanine (A) at amino acid position 55 to be replaced by an aspartic acid (D). 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