rs11151530

Variant names:

• chr18-69740648-A-G
• rs11151530
• NM_152721.6:c.738+1545A>G

Your query was ambiguous. Multiple possible variants found:

• chr18-69740648-A-G
• chr18-69740648-A-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DOK6	NM_152721.6	c.738+1545A>G		intron_variant	Intron 6 of 7	ENST00000382713.10	NP_689934.2
DOK6	XM_017025610.2	c.414+1545A>G		intron_variant	Intron 4 of 5		XP_016881099.1
DOK6	XM_017025611.2	c.414+1545A>G		intron_variant	Intron 4 of 5		XP_016881100.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DOK6	ENST00000382713.10	c.738+1545A>G		intron_variant	Intron 6 of 7	1	NM_152721.6	ENSP00000372160.5
DOK6	ENST00000577609.1	n.119+1545A>G		intron_variant	Intron 1 of 3	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

African (AFR) AF: 0.446 AC: 18493 AN: 41460

American (AMR) AF: 0.718 AC: 10978 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.713 AC: 2474 AN: 3472

East Asian (EAS) AF: 0.846 AC: 4382 AN: 5178

South Asian (SAS) AF: 0.778 AC: 3748 AN: 4816

European-Finnish (FIN) AF: 0.780 AC: 8245 AN: 10566

Middle Eastern (MID) AF: 0.767 AC: 224 AN: 292

European-Non Finnish (NFE) AF: 0.823 AC: 55990 AN: 67996

Other (OTH) AF: 0.725 AC: 1531 AN: 2112

Alfa AF: 0.746 Hom.: 5678

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
PhyloP100		-0.41
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs11151530; hg19: chr18-67407884;