rs10401068

Variant names:

• chr18-69595900-C-T
• rs10401068
• NM_152721.6:c.175-3484C>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.175-3484C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.452 in 151,842 control chromosomes in the GnomAD database, including 15,529 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 0.45 (15529 hom., cov: 32)
• Consequence: DOK6 NM_152721.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31
• Publications: 4 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]

ENSG00000265643 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.09).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_152721.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOK6	NM_152721.6	MANE Select	c.175-3484C>T		intron	N/A	NP_689934.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOK6	ENST00000382713.10	TSL:1 MANE Select	c.175-3484C>T		intron	N/A	ENSP00000372160.5
	ENSG00000265643	ENST00000583991.1	TSL:3	n.151+22644G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.453 AC: 68661 AN: 151724 Hom.: 15522 Cov.: 32

Gnomad AFR AF: 0.464

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.483

Gnomad EAS AF: 0.571

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.454

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.452 AC: 68704 AN: 151842 Hom.: 15529 Cov.: 32 AF XY: 0.451 AC XY: 33433 AN XY: 74196

African (AFR) AF: 0.464 AC: 19223 AN: 41398

American (AMR) AF: 0.429 AC: 6549 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.483 AC: 1678 AN: 3472

East Asian (EAS) AF: 0.572 AC: 2947 AN: 5152

South Asian (SAS) AF: 0.339 AC: 1638 AN: 4826

European-Finnish (FIN) AF: 0.454 AC: 4772 AN: 10514

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30209 AN: 67920

Other (OTH) AF: 0.472 AC: 996 AN: 2108

Alfa AF: 0.451 Hom.: 26079

Bravo AF: 0.456

Asia WGS AF: 0.456 AC: 1587 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	1.2
DANN	Benign	0.38
PhyloP100		-2.3
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: rs10401068; hg19: chr18-67263136;