12-49839006-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_181708.3(BCDIN3D):c.244G>A(p.Val82Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000212 in 1,612,240 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_181708.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCDIN3D | NM_181708.3 | c.244G>A | p.Val82Met | missense_variant | Exon 2 of 2 | ENST00000333924.6 | NP_859059.1 | |
BCDIN3D-AS1 | NR_027499.1 | n.940C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||
BCDIN3D-AS1 | NR_027501.1 | n.936C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||
BCDIN3D-AS1 | NR_027500.1 | n.570+366C>T | intron_variant | Intron 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000223 AC: 34AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 32AN: 250258Hom.: 0 AF XY: 0.000148 AC XY: 20AN XY: 135228
GnomAD4 exome AF: 0.000210 AC: 307AN: 1460096Hom.: 0 Cov.: 31 AF XY: 0.000193 AC XY: 140AN XY: 726230
GnomAD4 genome AF: 0.000223 AC: 34AN: 152144Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.244G>A (p.V82M) alteration is located in exon 2 (coding exon 2) of the BCDIN3D gene. This alteration results from a G to A substitution at nucleotide position 244, causing the valine (V) at amino acid position 82 to be replaced by a methionine (M). 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