rs9517474

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001366683.2(DOCK9):​c.2469+36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.765 in 1,437,178 control chromosomes in the GnomAD database, including 424,555 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.71 ( 39088 hom., cov: 33)
Exomes 𝑓: 0.77 ( 385467 hom. )

Consequence

DOCK9
NM_001366683.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.233
Variant links:
Genes affected
DOCK9 (HGNC:14132): (dedicator of cytokinesis 9) Enables cadherin binding activity. Predicted to be involved in positive regulation of GTPase activity. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DOCK9NM_001366683.2 linkc.2469+36C>T intron_variant Intron 22 of 52 ENST00000682017.1 NP_001353612.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DOCK9ENST00000682017.1 linkc.2469+36C>T intron_variant Intron 22 of 52 NM_001366683.2 ENSP00000507034.1 A0A804HIE8

Frequencies

GnomAD3 genomes
AF:
0.709
AC:
107751
AN:
151982
Hom.:
39070
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.575
Gnomad AMI
AF:
0.845
Gnomad AMR
AF:
0.754
Gnomad ASJ
AF:
0.786
Gnomad EAS
AF:
0.523
Gnomad SAS
AF:
0.872
Gnomad FIN
AF:
0.719
Gnomad MID
AF:
0.896
Gnomad NFE
AF:
0.773
Gnomad OTH
AF:
0.758
GnomAD3 exomes
AF:
0.751
AC:
143063
AN:
190576
Hom.:
54523
AF XY:
0.760
AC XY:
77823
AN XY:
102454
show subpopulations
Gnomad AFR exome
AF:
0.574
Gnomad AMR exome
AF:
0.771
Gnomad ASJ exome
AF:
0.792
Gnomad EAS exome
AF:
0.525
Gnomad SAS exome
AF:
0.885
Gnomad FIN exome
AF:
0.726
Gnomad NFE exome
AF:
0.777
Gnomad OTH exome
AF:
0.772
GnomAD4 exome
AF:
0.772
AC:
992108
AN:
1285078
Hom.:
385467
Cov.:
16
AF XY:
0.775
AC XY:
496744
AN XY:
641054
show subpopulations
Gnomad4 AFR exome
AF:
0.566
Gnomad4 AMR exome
AF:
0.767
Gnomad4 ASJ exome
AF:
0.797
Gnomad4 EAS exome
AF:
0.588
Gnomad4 SAS exome
AF:
0.882
Gnomad4 FIN exome
AF:
0.728
Gnomad4 NFE exome
AF:
0.779
Gnomad4 OTH exome
AF:
0.766
GnomAD4 genome
AF:
0.709
AC:
107808
AN:
152100
Hom.:
39088
Cov.:
33
AF XY:
0.709
AC XY:
52688
AN XY:
74358
show subpopulations
Gnomad4 AFR
AF:
0.575
Gnomad4 AMR
AF:
0.754
Gnomad4 ASJ
AF:
0.786
Gnomad4 EAS
AF:
0.523
Gnomad4 SAS
AF:
0.872
Gnomad4 FIN
AF:
0.719
Gnomad4 NFE
AF:
0.773
Gnomad4 OTH
AF:
0.761
Alfa
AF:
0.771
Hom.:
91858
Bravo
AF:
0.708
Asia WGS
AF:
0.734
AC:
2548
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
2.0
DANN
Benign
0.38

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: rs9517474; hg19: chr13-99536031; API