rs139753457

Positions:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_173660.5(DOK7):​c.772+37G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00296 in 1,558,414 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0025 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0030 ( 12 hom. )

Consequence

DOK7
NM_173660.5 intron

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.62
Variant links:
Genes affected
DOK7 (HGNC:26594): (docking protein 7) The protein encoded by this gene is essential for neuromuscular synaptogenesis. The protein functions in aneural activation of muscle-specific receptor kinase, which is required for postsynaptic differentiation, and in the subsequent clustering of the acetylcholine receptor in myotubes. This protein can also induce autophosphorylation of muscle-specific receptor kinase. Mutations in this gene are a cause of familial limb-girdle myasthenia autosomal recessive, which is also known as congenital myasthenic syndrome type 1B. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
Variant 4-3489833-G-A is Benign according to our data. Variant chr4-3489833-G-A is described in ClinVar as [Benign]. Clinvar id is 262888.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population amr. gnomad4 allele frequency = 0.00248 (377/152158) while in subpopulation AMR AF= 0.00477 (73/15290). AF 95% confidence interval is 0.00389. There are 0 homozygotes in gnomad4. There are 176 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 12 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
DOK7NM_173660.5 linkuse as main transcriptc.772+37G>A intron_variant ENST00000340083.6 NP_775931.3 Q18PE1-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
DOK7ENST00000340083.6 linkuse as main transcriptc.772+37G>A intron_variant 1 NM_173660.5 ENSP00000344432.5 Q18PE1-1

Frequencies

GnomAD3 genomes
AF:
0.00248
AC:
377
AN:
152040
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000556
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00478
Gnomad ASJ
AF:
0.00317
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000565
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00375
Gnomad OTH
AF:
0.00430
GnomAD3 exomes
AF:
0.00277
AC:
453
AN:
163738
Hom.:
3
AF XY:
0.00270
AC XY:
235
AN XY:
87028
show subpopulations
Gnomad AFR exome
AF:
0.000735
Gnomad AMR exome
AF:
0.00287
Gnomad ASJ exome
AF:
0.00388
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00111
Gnomad FIN exome
AF:
0.000526
Gnomad NFE exome
AF:
0.00438
Gnomad OTH exome
AF:
0.00527
GnomAD4 exome
AF:
0.00301
AC:
4233
AN:
1406256
Hom.:
12
Cov.:
32
AF XY:
0.00299
AC XY:
2076
AN XY:
694172
show subpopulations
Gnomad4 AFR exome
AF:
0.000528
Gnomad4 AMR exome
AF:
0.00297
Gnomad4 ASJ exome
AF:
0.00413
Gnomad4 EAS exome
AF:
0.0000273
Gnomad4 SAS exome
AF:
0.00116
Gnomad4 FIN exome
AF:
0.000663
Gnomad4 NFE exome
AF:
0.00339
Gnomad4 OTH exome
AF:
0.00309
GnomAD4 genome
AF:
0.00248
AC:
377
AN:
152158
Hom.:
0
Cov.:
32
AF XY:
0.00237
AC XY:
176
AN XY:
74408
show subpopulations
Gnomad4 AFR
AF:
0.000554
Gnomad4 AMR
AF:
0.00477
Gnomad4 ASJ
AF:
0.00317
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000565
Gnomad4 NFE
AF:
0.00375
Gnomad4 OTH
AF:
0.00426
Alfa
AF:
0.00383
Hom.:
1
Bravo
AF:
0.00293
Asia WGS
AF:
0.000289
AC:
1
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
not provided Benign:1
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.88
CADD
Benign
0.46
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: rs139753457; hg19: chr4-3491560; API