rs3918143
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_005104.4(BRD2):c.1421C>T(p.Ala474Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0308 in 1,613,002 control chromosomes in the GnomAD database, including 859 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_005104.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BRD2 | NM_005104.4 | c.1421C>T | p.Ala474Val | missense_variant | 9/13 | ENST00000374825.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BRD2 | ENST00000374825.9 | c.1421C>T | p.Ala474Val | missense_variant | 9/13 | 1 | NM_005104.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0237 AC: 3597AN: 152078Hom.: 63 Cov.: 32
GnomAD3 exomes AF: 0.0293 AC: 7213AN: 246574Hom.: 126 AF XY: 0.0305 AC XY: 4100AN XY: 134380
GnomAD4 exome AF: 0.0315 AC: 46009AN: 1460806Hom.: 796 Cov.: 63 AF XY: 0.0321 AC XY: 23328AN XY: 726720
GnomAD4 genome ? AF: 0.0236 AC: 3597AN: 152196Hom.: 63 Cov.: 32 AF XY: 0.0231 AC XY: 1720AN XY: 74406
ClinVar
Submissions by phenotype
BRD2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at