18-54591232-C-T

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

Scores

3
4

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.618
Variant links:
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
DYNAPNM_001307955.1 linkc.37C>T p.Gln13* stop_gained Exon 2 of 3 NP_001294884.1 K7EMN5
DYNAPXM_011525923.4 linkc.37C>T p.Gln13* stop_gained Exon 3 of 5 XP_011524225.1
DYNAPXM_017025709.2 linkc.37C>T p.Gln13* stop_gained Exon 3 of 4 XP_016881198.1 K7EMN5
DYNAPNM_173629.3 linkc.-51C>T upstream_gene_variant ENST00000648945.2 NP_775900.2 Q8N1N2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DYNAPENST00000321600.1 linkc.28C>T p.Gln10* stop_gained Exon 1 of 3 2 ENSP00000315265.1 Q8N1N2
DYNAPENST00000585973.1 linkc.37C>T p.Gln13* stop_gained Exon 2 of 3 3 ENSP00000466577.1 K7EMN5
DYNAPENST00000648945.2 linkc.-51C>T upstream_gene_variant NM_173629.3 ENSP00000496812.1 A0A3B3IRJ4

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000400
AC:
1
AN:
249768
Hom.:
0
AF XY:
0.00000741
AC XY:
1
AN XY:
135008
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000885
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000343
AC:
5
AN:
1459652
Hom.:
0
Cov.:
30
AF XY:
0.00000551
AC XY:
4
AN XY:
726076
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000450
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Uncertain
0.13
D
BayesDel_noAF
Uncertain
-0.050
CADD
Benign
0.36
DANN
Uncertain
0.99
Eigen
Benign
0.040
Eigen_PC
Benign
-0.37
FATHMM_MKL
Benign
0.0083
N
Vest4
0.25
GERP RS
-1.8

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1413477736; hg19: chr18-52258463; API