rs199578351

chr4-3476338-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_173660.5(DOK7):c.332-4G>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00142 in 1,384,606 control chromosomes in the GnomAD database, including 67 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.0073 (42 hom., cov: 30)
  • Exomes 𝑓: 0.00081 (25 hom.)
• Consequence: DOK7 NM_173660.5 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.00002415
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:4
• Conservation: PhyloP100: -1.89

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]

LOC105374355 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 4-3476338-G-A is Benign according to our data. Variant chr4-3476338-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 128912.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00733 (950/129618) while in subpopulation AFR AF= 0.0265 (909/34348). AF 95% confidence interval is 0.025. There are 42 homozygotes in gnomad4. There are 457 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 41 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOK7	NM_173660.5	c.332-4G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000340083.6
LOC105374355	XR_007057994.1	n.828C>T		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOK7	ENST00000340083.6	c.332-4G>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		1	NM_173660.5	P1

Frequencies

GnomAD3 genomes AF: 0.00731 AC: 947 AN: 129540 Hom.: 41 Cov.: 30

Gnomad AFR AF: 0.0264

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00285

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000282

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000161

Gnomad OTH AF: 0.00352

GnomAD3 exomes AF: 0.00201 AC: 481 AN: 239618 Hom.: 24 AF XY: 0.00129 AC XY: 168 AN XY: 130640

Gnomad AFR exome AF: 0.0294

Gnomad AMR exome AF: 0.00131

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000138

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00000924

Gnomad OTH exome AF: 0.000344

GnomAD4 exome AF: 0.000811 AC: 1018 AN: 1254988 Hom.: 25 Cov.: 39 AF XY: 0.000681 AC XY: 424 AN XY: 622268

Gnomad4 AFR exome AF: 0.0299

Gnomad4 AMR exome AF: 0.00182

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000713

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000921

Gnomad4 OTH exome AF: 0.00221

GnomAD4 genome AF: 0.00733 AC: 950 AN: 129618 Hom.: 42 Cov.: 30 AF XY: 0.00736 AC XY: 457 AN XY: 62078

Gnomad4 AFR AF: 0.0265

Gnomad4 AMR AF: 0.00284

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000282

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000161

Gnomad4 OTH AF: 0.00348

Alfa AF: 0.00330 Hom.: 4

Bravo AF: 0.00835

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:2

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Fetal akinesia deformation sequence 1;C1850792:Congenital myasthenic syndrome 10 Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 26, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.82
Dann	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000024
dbscSNV1_RF	Benign	0.0
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

Other links and lift over

dbSNP: rs199578351; hg19: chr4-3478065;