rs11151530

chr18-69740648-A-Gchr18-69740648-A-T

Variant summary

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

The NM_152721.6(DOK6):c.738+1545A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,082 control chromosomes in the GnomAD database, including 39,536 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 0.70 (39536 hom., cov: 32)
• Consequence: DOK6 NM_152721.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.411

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DOK6	NM_152721.6	c.738+1545A>G		intron_variant		ENST00000382713.10
DOK6	XM_017025610.2	c.414+1545A>G		intron_variant
DOK6	XM_017025611.2	c.414+1545A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DOK6	ENST00000382713.10	c.738+1545A>G		intron_variant		1	NM_152721.6	P1
DOK6	ENST00000577609.1	n.119+1545A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106797 AN: 151964 Hom.: 39535 Cov.: 32

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.713

Gnomad EAS AF: 0.846

Gnomad SAS AF: 0.779

Gnomad FIN AF: 0.780

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.702 AC: 106825 AN: 152082 Hom.: 39536 Cov.: 32 AF XY: 0.704 AC XY: 52332 AN XY: 74354

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.718

Gnomad4 ASJ AF: 0.713

Gnomad4 EAS AF: 0.846

Gnomad4 SAS AF: 0.778

Gnomad4 FIN AF: 0.780

Gnomad4 NFE AF: 0.823

Gnomad4 OTH AF: 0.725

Alfa AF: 0.757 Hom.: 5595

Bravo AF: 0.686

Asia WGS AF: 0.794 AC: 2756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.8
Dann	Benign	0.71

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: rs11151530; hg19: chr18-67407884;