chr1-32212092-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001099434.2(DCDC2B):c.418G>A(p.Val140Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,613,800 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001099434.2 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DCDC2B | NM_001099434.2 | c.418G>A | p.Val140Ile | missense_variant | 4/9 | ENST00000409358.2 | NP_001092904.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DCDC2B | ENST00000409358.2 | c.418G>A | p.Val140Ile | missense_variant | 4/9 | 1 | NM_001099434.2 | ENSP00000386870.1 | ||
DCDC2B | ENST00000487056.1 | n.648G>A | non_coding_transcript_exon_variant | 3/7 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249068Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135130
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461534Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 727020
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74448
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 28, 2024 | The c.418G>A (p.V140I) alteration is located in exon 4 (coding exon 4) of the DCDC2B gene. This alteration results from a G to A substitution at nucleotide position 418, causing the valine (V) at amino acid position 140 to be replaced by an isoleucine (I). 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