rs9319790

chr18-69638045-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_152721.6(DOK6):c.289+38547C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0925 in 152,134 control chromosomes in the GnomAD database, including 742 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 0.092 (742 hom., cov: 32)
• Consequence: DOK6 NM_152721.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

Genes affected

DOK6 (HGNC:28301): (docking protein 6) DOK6 is a member of the DOK (see DOK1; MIM 602919) family of intracellular adaptors that play a role in the RET (MIM 164761) signaling cascade (Crowder et al., 2004 [PubMed 15286081]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOK6	NM_152721.6	c.289+38547C>T		intron_variant		ENST00000382713.10
DOK6	XM_017025610.2	c.-5781C>T		5_prime_UTR_variant	1/6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOK6	ENST00000382713.10	c.289+38547C>T		intron_variant		1	NM_152721.6	P1

Frequencies

GnomAD3 genomes AF: 0.0924 AC: 14040 AN: 152016 Hom.: 745 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.110

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0839

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0678

Gnomad FIN AF: 0.0454

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.0686

Gnomad OTH AF: 0.110

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0925 AC: 14068 AN: 152134 Hom.: 742 Cov.: 32 AF XY: 0.0931 AC XY: 6923 AN XY: 74372

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.0839

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0683

Gnomad4 FIN AF: 0.0454

Gnomad4 NFE AF: 0.0686

Gnomad4 OTH AF: 0.113

Alfa AF: 0.0825 Hom.: 1060

Bravo AF: 0.104

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	5.9
Dann	Benign	0.81

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: rs9319790; hg19: chr18-67305281;