18-54591232-C-T
Variant names:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001307955.1(DYNAP):c.37C>T(p.Gln13*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,459,652 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000034 ( 0 hom. )
Consequence
DYNAP
NM_001307955.1 stop_gained
NM_001307955.1 stop_gained
Scores
3
4
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.618
Genes affected
DYNAP (HGNC:26808): (dynactin associated protein) Involved in several processes, including activation of protein kinase B activity; cellular response to ergosterol; and positive regulation of cell population proliferation. Located in Golgi apparatus and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DYNAP | NM_001307955.1 | c.37C>T | p.Gln13* | stop_gained | Exon 2 of 3 | NP_001294884.1 | ||
DYNAP | XM_011525923.4 | c.37C>T | p.Gln13* | stop_gained | Exon 3 of 5 | XP_011524225.1 | ||
DYNAP | XM_017025709.2 | c.37C>T | p.Gln13* | stop_gained | Exon 3 of 4 | XP_016881198.1 | ||
DYNAP | NM_173629.3 | c.-51C>T | upstream_gene_variant | ENST00000648945.2 | NP_775900.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DYNAP | ENST00000321600.1 | c.28C>T | p.Gln10* | stop_gained | Exon 1 of 3 | 2 | ENSP00000315265.1 | |||
DYNAP | ENST00000585973.1 | c.37C>T | p.Gln13* | stop_gained | Exon 2 of 3 | 3 | ENSP00000466577.1 | |||
DYNAP | ENST00000648945.2 | c.-51C>T | upstream_gene_variant | NM_173629.3 | ENSP00000496812.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249768Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 135008
GnomAD3 exomes
AF:
AC:
1
AN:
249768
Hom.:
AF XY:
AC XY:
1
AN XY:
135008
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459652Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 726076
GnomAD4 exome
AF:
AC:
5
AN:
1459652
Hom.:
Cov.:
30
AF XY:
AC XY:
4
AN XY:
726076
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at