chr5-135447063-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_130848.3(DCANP1):c.46G>A(p.Gly16Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000198 in 1,613,888 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_130848.3 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 | UniProt |
---|---|---|---|---|---|---|---|
DCANP1 | NM_130848.3 | c.46G>A | p.Gly16Ser | missense_variant | 1/1 | ENST00000503143.3 | |
TIFAB | NM_001099221.2 | c.*2391G>A | 3_prime_UTR_variant | 2/2 | ENST00000537858.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DCANP1 | ENST00000503143.3 | c.46G>A | p.Gly16Ser | missense_variant | 1/1 | NM_130848.3 | P1 | ||
TIFAB | ENST00000537858.2 | c.*2391G>A | 3_prime_UTR_variant | 2/2 | 1 | NM_001099221.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 250914Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135618
GnomAD4 exome AF: 0.0000198 AC: 29AN: 1461690Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727126
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 21, 2022 | The c.46G>A (p.G16S) alteration is located in exon 1 (coding exon 1) of the DCANP1 gene. This alteration results from a G to A substitution at nucleotide position 46, causing the glycine (G) at amino acid position 16 to be replaced by a serine (S). 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