rs12048208

Variant summary

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

The NM_001367561.1(DOCK7):​c.1683-2985C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.126 in 151,224 control chromosomes in the GnomAD database, including 1,291 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 0.13 ( 1291 hom., cov: 31)

Consequence

DOCK7
NM_001367561.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.344
Variant links:
Genes affected
DOCK7 (HGNC:19190): (dedicator of cytokinesis 7) The protein encoded by this gene is a guanine nucleotide exchange factor (GEF) that plays a role in axon formation and neuronal polarization. The encoded protein displays GEF activity toward RAC1 and RAC3 Rho small GTPases but not toward CDC42. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

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=-0.96).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
DOCK7NM_001367561.1 linkuse as main transcriptc.1683-2985C>T intron_variant ENST00000635253.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
DOCK7ENST00000635253.2 linkuse as main transcriptc.1683-2985C>T intron_variant 5 NM_001367561.1 Q96N67-1

Frequencies

GnomAD3 genomes
AF:
0.126
AC:
18996
AN:
151110
Hom.:
1285
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.122
Gnomad AMI
AF:
0.203
Gnomad AMR
AF:
0.111
Gnomad ASJ
AF:
0.0895
Gnomad EAS
AF:
0.178
Gnomad SAS
AF:
0.255
Gnomad FIN
AF:
0.0894
Gnomad MID
AF:
0.136
Gnomad NFE
AF:
0.125
Gnomad OTH
AF:
0.117
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.126
AC:
19022
AN:
151224
Hom.:
1291
Cov.:
31
AF XY:
0.126
AC XY:
9294
AN XY:
73812
show subpopulations
Gnomad4 AFR
AF:
0.122
Gnomad4 AMR
AF:
0.111
Gnomad4 ASJ
AF:
0.0895
Gnomad4 EAS
AF:
0.178
Gnomad4 SAS
AF:
0.254
Gnomad4 FIN
AF:
0.0894
Gnomad4 NFE
AF:
0.125
Gnomad4 OTH
AF:
0.125
Alfa
AF:
0.125
Hom.:
2567
Bravo
AF:
0.126
Asia WGS
AF:
0.246
AC:
853
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.96
CADD
Benign
0.44
DANN
Benign
0.48

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: rs12048208; hg19: chr1-63055280; API