16-3031047-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_001369667.1(BICDL2):c.386G>A(p.Arg129Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0034 in 1,540,310 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001369667.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BICDL2 | NM_001369667.1 | c.386G>A | p.Arg129Gln | missense_variant | Exon 3 of 10 | ENST00000572449.6 | NP_001356596.1 | |
BICDL2 | NM_001103175.2 | c.386G>A | p.Arg129Gln | missense_variant | Exon 2 of 9 | NP_001096645.1 | ||
BICDL2 | XM_005255135.5 | c.386G>A | p.Arg129Gln | missense_variant | Exon 3 of 10 | XP_005255192.1 | ||
BICDL2 | XM_011522391.3 | c.191G>A | p.Arg64Gln | missense_variant | Exon 2 of 9 | XP_011520693.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00231 AC: 351AN: 152234Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.00259 AC: 365AN: 141182Hom.: 0 AF XY: 0.00237 AC XY: 181AN XY: 76246
GnomAD4 exome AF: 0.00352 AC: 4887AN: 1387958Hom.: 11 Cov.: 32 AF XY: 0.00340 AC XY: 2331AN XY: 685414
GnomAD4 genome AF: 0.00230 AC: 351AN: 152352Hom.: 1 Cov.: 33 AF XY: 0.00205 AC XY: 153AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
BICDL2: BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at