3-53312377-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018403.7(DCP1A):c.374T>C(p.Val125Ala) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.0000183 in 1,585,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018403.7 missense, splice_region
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DCP1A | NM_018403.7 | c.374T>C | p.Val125Ala | missense_variant, splice_region_variant | 5/10 | ENST00000610213.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCP1A | ENST00000610213.6 | c.374T>C | p.Val125Ala | missense_variant, splice_region_variant | 5/10 | 1 | NM_018403.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 151984Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000861 AC: 19AN: 220646Hom.: 0 AF XY: 0.0000583 AC XY: 7AN XY: 120114
GnomAD4 exome AF: 0.0000167 AC: 24AN: 1433018Hom.: 0 Cov.: 30 AF XY: 0.0000126 AC XY: 9AN XY: 711530
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152100Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 03, 2023 | The c.374T>C (p.V125A) alteration is located in exon 5 (coding exon 5) of the DCP1A gene. This alteration results from a T to C substitution at nucleotide position 374, causing the valine (V) at amino acid position 125 to be replaced by an alanine (A). 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