chr1-62487702-G-A

Position:

• chr1-62487702-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001367561.1(DOCK7):​c.5494-290C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 293,872 control chromosomes in the GnomAD database, including 7,608 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.20 (3462 hom., cov: 32)
  • Exomes 𝑓: 0.23 (4146 hom.)
• Consequence: DOCK7 NM_001367561.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.74

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 1-62487702-G-A is Benign according to our data. Variant chr1-62487702-G-A is described in ClinVar as [Benign]. Clinvar id is 1294572.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DOCK7	NM_001367561.1	c.5494-290C>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.5494-290C>T		intron_variant		5	NM_001367561.1	ENSP00000489124

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30068 AN: 151912 Hom.: 3456 Cov.: 32

Gnomad AFR AF: 0.0721

Gnomad AMI AF: 0.164

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.215

GnomAD4 exome AF: 0.231 AC: 32765 AN: 141840 Hom.: 4146 Cov.: 0 AF XY: 0.229 AC XY: 16756 AN XY: 73148

Gnomad4 AFR exome AF: 0.0691

Gnomad4 AMR exome AF: 0.210

Gnomad4 ASJ exome AF: 0.224

Gnomad4 EAS exome AF: 0.152

Gnomad4 SAS exome AF: 0.190

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.255

Gnomad4 OTH exome AF: 0.233

GnomAD4 genome AF: 0.198 AC: 30087 AN: 152032 Hom.: 3462 Cov.: 32 AF XY: 0.199 AC XY: 14794 AN XY: 74300

Gnomad4 AFR AF: 0.0722

Gnomad4 AMR AF: 0.230

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.139

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.256

Gnomad4 OTH AF: 0.212

Alfa AF: 0.243 Hom.: 6233

Bravo AF: 0.186

Asia WGS AF: 0.168 AC: 583 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 08, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.079
DANN	Benign	0.45

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: rs10493326; hg19: chr1-62953373;