rs2031373

Variant names:

• chr1-62617618-C-A
• rs2031373
• NM_001367561.1:c.1682+1088G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

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 Gene-Disease associations (from GenCC):

• genetic developmental and epileptic encephalopathy

  Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
• developmental and epileptic encephalopathy, 23

  Inheritance: AR Classification: STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Orphanet, G2P

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
DOCK7	NM_001367561.1	c.1682+1088G>T		intron_variant	Intron 14 of 49	ENST00000635253.2	NP_001354490.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DOCK7	ENST00000635253.2	c.1682+1088G>T		intron_variant	Intron 14 of 49	5	NM_001367561.1	ENSP00000489124.1

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

African (AFR) AF: 0.738 AC: 30589 AN: 41448

American (AMR) AF: 0.628 AC: 9560 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3466

East Asian (EAS) AF: 0.388 AC: 1996 AN: 5148

South Asian (SAS) AF: 0.653 AC: 3140 AN: 4812

European-Finnish (FIN) AF: 0.551 AC: 5809 AN: 10534

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.599 AC: 40601 AN: 67730

Other (OTH) AF: 0.583 AC: 1230 AN: 2108

Alfa AF: 0.601 Hom.: 102399

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
PhyloP100		-0.30
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: rs2031373; hg19: chr1-63083289;