12-49838477-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_181708.3(BCDIN3D):c.773G>A(p.Ser258Asn) variant causes a missense change. The variant allele was found at a frequency of 0.0000768 in 1,613,992 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BCDIN3D | NM_181708.3 | c.773G>A | p.Ser258Asn | missense_variant | Exon 2 of 2 | ENST00000333924.6 | NP_859059.1 | |
BCDIN3D-AS1 | NR_027499.1 | n.411C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | ||||
BCDIN3D-AS1 | NR_027500.1 | n.407C>T | non_coding_transcript_exon_variant | Exon 3 of 4 | ||||
BCDIN3D-AS1 | NR_027501.1 | n.407C>T | non_coding_transcript_exon_variant | Exon 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249008Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134798
GnomAD4 exome AF: 0.0000821 AC: 120AN: 1461824Hom.: 0 Cov.: 31 AF XY: 0.0000853 AC XY: 62AN XY: 727214
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.773G>A (p.S258N) 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 773, causing the serine (S) at amino acid position 258 to be replaced by an asparagine (N). 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