rs2031373

Positions:

• chr1-62617618-C-A
• chr1-62617618-C-G
• chr1-62617618-C-T

Variant summary

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

The NM_001367561.1(DOCK7):​c.1682+1088G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 151,684 control chromosomes in the GnomAD database, including 30,380 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 0.63 (30380 hom., cov: 32)
• Consequence: DOCK7 NM_001367561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.300

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK7	NM_001367561.1	c.1682+1088G>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.1682+1088G>T		intron_variant		5	NM_001367561.1	ENSP00000489124

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95116 AN: 151566 Hom.: 30316 Cov.: 32

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.570

Gnomad AMR AF: 0.627

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.387

Gnomad SAS AF: 0.652

Gnomad FIN AF: 0.551

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.628 AC: 95245 AN: 151684 Hom.: 30380 Cov.: 32 AF XY: 0.626 AC XY: 46421 AN XY: 74132

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.628

Gnomad4 ASJ AF: 0.477

Gnomad4 EAS AF: 0.388

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.551

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.583

Alfa AF: 0.590 Hom.: 40170

Bravo AF: 0.632

Asia WGS AF: 0.613 AC: 2131 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.49
DANN	Benign	0.24

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: rs2031373; hg19: chr1-63083289;