chr16-2210005-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_182563.4(BRICD5):c.383G>A(p.Arg128His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000923 in 1,560,330 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182563.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BRICD5 | NM_182563.4 | c.383G>A | p.Arg128His | missense_variant | Exon 4 of 6 | ENST00000328540.8 | NP_872369.2 | |
BRICD5 | XM_047433958.1 | c.383G>A | p.Arg128His | missense_variant | Exon 4 of 5 | XP_047289914.1 | ||
BRICD5 | XM_047433959.1 | c.449G>A | p.Arg150His | 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.383G>A | p.Arg128His | missense_variant | Exon 4 of 6 | 1 | NM_182563.4 | ENSP00000332389.3 | ||
BRICD5 | ENST00000562360.5 | c.383G>A | p.Arg128His | missense_variant | Exon 4 of 5 | 2 | ENSP00000455052.1 | |||
BRICD5 | ENST00000566018.1 | c.457G>A | p.Ala153Thr | missense_variant | Exon 3 of 3 | 2 | ENSP00000457969.1 | |||
BRICD5 | ENST00000566795.1 | n.141G>A | non_coding_transcript_exon_variant | Exon 1 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152192Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000131 AC: 28AN: 213466Hom.: 0 AF XY: 0.000192 AC XY: 22AN XY: 114576
GnomAD4 exome AF: 0.0000987 AC: 139AN: 1408138Hom.: 1 Cov.: 33 AF XY: 0.000128 AC XY: 89AN XY: 693020
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152192Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.383G>A (p.R128H) alteration is located in exon 4 (coding exon 4) of the BRICD5 gene. This alteration results from a G to A substitution at nucleotide position 383, causing the arginine (R) at amino acid position 128 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