16-2209972-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_182563.4(BRICD5):c.416G>A(p.Arg139Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000202 in 1,535,090 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_182563.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BRICD5 | NM_182563.4 | c.416G>A | p.Arg139Gln | missense_variant | Exon 4 of 6 | ENST00000328540.8 | NP_872369.2 | |
BRICD5 | XM_047433958.1 | c.416G>A | p.Arg139Gln | missense_variant | Exon 4 of 5 | XP_047289914.1 | ||
BRICD5 | XM_047433959.1 | c.482G>A | p.Arg161Gln | missense_variant | Exon 2 of 4 | XP_047289915.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BRICD5 | ENST00000328540.8 | c.416G>A | p.Arg139Gln | missense_variant | Exon 4 of 6 | 1 | NM_182563.4 | ENSP00000332389.3 | ||
BRICD5 | ENST00000562360.5 | c.416G>A | p.Arg139Gln | missense_variant | Exon 4 of 5 | 2 | ENSP00000455052.1 | |||
BRICD5 | ENST00000566795.1 | n.174G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 | |||||
BRICD5 | ENST00000566018.1 | c.*28G>A | downstream_gene_variant | 2 | ENSP00000457969.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000317 AC: 6AN: 189400Hom.: 0 AF XY: 0.00000993 AC XY: 1AN XY: 100706
GnomAD4 exome AF: 0.0000195 AC: 27AN: 1382780Hom.: 0 Cov.: 33 AF XY: 0.0000177 AC XY: 12AN XY: 678266
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152310Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:1
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at