rs1168029

Positions:

• chr1-62503731-G-A
• chr1-62503731-G-C

Variant summary

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

The NM_001367561.1(DOCK7):​c.4764+899C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 151,830 control chromosomes in the GnomAD database, including 26,786 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 0.57 (26786 hom., cov: 31)
• Consequence: DOCK7 NM_001367561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

DOCK7 (HGNC:19190): (dedicator of cytokinesis 7) The protein encoded by this gene is a guanine nucleotide exchange factor (GEF) that plays a role in axon formation and neuronal polarization. The encoded protein displays GEF activity toward RAC1 and RAC3 Rho small GTPases but not toward CDC42. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2012]

DOCK7 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.737 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK7	NM_001367561.1	c.4764+899C>T		intron_variant		ENST00000635253.2	NP_001354490.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DOCK7	ENST00000635253.2	c.4764+899C>T		intron_variant		5	NM_001367561.1	ENSP00000489124.1

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87239 AN: 151712 Hom.: 26788 Cov.: 31

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.595

Gnomad AMR AF: 0.607

Gnomad ASJ AF: 0.758

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.661

Gnomad OTH AF: 0.638

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

GnomAD4 genome AF: 0.575 AC: 87253 AN: 151830 Hom.: 26786 Cov.: 31 AF XY: 0.576 AC XY: 42753 AN XY: 74174

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.607

Gnomad4 ASJ AF: 0.758

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.538

Gnomad4 FIN AF: 0.728

Gnomad4 NFE AF: 0.661

Gnomad4 OTH AF: 0.630

Alfa AF: 0.657 Hom.: 25948

Bravo AF: 0.558

Asia WGS AF: 0.555 AC: 1928 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.44

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: rs1168029; hg19: chr1-62969402;