4-3473380-G-C

Variant names:

• chr4-3473380-G-C
• rs2344208
• NM_173660.5:c.101-26G>C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_173660.5(DOK7):​c.101-26G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.165 in 1,607,178 control chromosomes in the GnomAD database, including 26,272 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.23 (5174 hom., cov: 34)
  • Exomes 𝑓: 0.16 (21098 hom.)
• Consequence: DOK7 NM_173660.5 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:3
• Conservation: PhyloP100: -1.10

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]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 4-3473380-G-C is Benign according to our data. Variant chr4-3473380-G-C is described in ClinVar as [Benign]. Clinvar id is 262865.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DOK7	NM_173660.5	c.101-26G>C		intron_variant	Intron 2 of 6	ENST00000340083.6	NP_775931.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DOK7	ENST00000340083.6	c.101-26G>C		intron_variant	Intron 2 of 6	1	NM_173660.5	ENSP00000344432.5

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35230 AN: 152088 Hom.: 5157 Cov.: 34

Gnomad AFR AF: 0.412

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.238

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.203

GnomAD3 exomes AF: 0.197 AC: 46805 AN: 237486 Hom.: 5695 AF XY: 0.186 AC XY: 24326 AN XY: 130668

Gnomad AFR exome AF: 0.415

Gnomad AMR exome AF: 0.320

Gnomad ASJ exome AF: 0.112

Gnomad EAS exome AF: 0.297

Gnomad SAS exome AF: 0.157

Gnomad FIN exome AF: 0.130

Gnomad NFE exome AF: 0.145

Gnomad OTH exome AF: 0.173

GnomAD4 exome AF: 0.158 AC: 230210 AN: 1454972 Hom.: 21098 Cov.: 33 AF XY: 0.157 AC XY: 113621 AN XY: 723782

Gnomad4 AFR exome AF: 0.428

Gnomad4 AMR exome AF: 0.307

Gnomad4 ASJ exome AF: 0.109

Gnomad4 EAS exome AF: 0.317

Gnomad4 SAS exome AF: 0.161

Gnomad4 FIN exome AF: 0.130

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.167

GnomAD4 genome AF: 0.232 AC: 35285 AN: 152206 Hom.: 5174 Cov.: 34 AF XY: 0.231 AC XY: 17207 AN XY: 74404

Gnomad4 AFR AF: 0.412

Gnomad4 AMR AF: 0.238

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.162

Gnomad4 FIN AF: 0.133

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.200

Alfa AF: 0.114 Hom.: 173

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

-

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 19, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not specified Benign:1

-

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.074
DANN	Benign	0.29

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

Other links and lift over

dbSNP: rs2344208; hg19: chr4-3475107; COSMIC: COSV60773875;