NM_001367561.1:c.5508+2211G>A

Variant names:

• chr1-62485187-C-T
• rs10889332
• NM_001367561.1:c.5508+2211G>A

Variant summary

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

The NM_001367561.1(DOCK7):​c.5508+2211G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.362 in 984,404 control chromosomes in the GnomAD database, including 65,663 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 0.38 (11968 hom., cov: 32)
  • Exomes 𝑓: 0.36 (53695 hom.)
• Consequence: DOCK7 NM_001367561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.524 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DOCK7	NM_001367561.1	c.5508+2211G>A		intron_variant	Intron 43 of 49	ENST00000635253.2	NP_001354490.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DOCK7	ENST00000635253.2	c.5508+2211G>A		intron_variant	Intron 43 of 49	5	NM_001367561.1	ENSP00000489124.1

Frequencies

GnomAD3 genomes AF: 0.384 AC: 58304 AN: 151648 Hom.: 11944 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.402

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.245

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.252

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.333

GnomAD4 exome AF: 0.358 AC: 297755 AN: 832640 Hom.: 53695 Cov.: 30 AF XY: 0.358 AC XY: 137660 AN XY: 384526

Gnomad4 AFR exome AF: 0.548

Gnomad4 AMR exome AF: 0.377

Gnomad4 ASJ exome AF: 0.227

Gnomad4 EAS exome AF: 0.252

Gnomad4 SAS exome AF: 0.458

Gnomad4 FIN exome AF: 0.268

Gnomad4 NFE exome AF: 0.353

Gnomad4 OTH exome AF: 0.357

GnomAD4 genome AF: 0.385 AC: 58378 AN: 151764 Hom.: 11968 Cov.: 32 AF XY: 0.384 AC XY: 28443 AN XY: 74138

Gnomad4 AFR AF: 0.530

Gnomad4 AMR AF: 0.377

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.246

Gnomad4 SAS AF: 0.449

Gnomad4 FIN AF: 0.252

Gnomad4 NFE AF: 0.334

Gnomad4 OTH AF: 0.341

Alfa AF: 0.356 Hom.: 3077

Bravo AF: 0.397

Asia WGS AF: 0.434 AC: 1512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.58
DANN	Benign	0.57

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: rs10889332; hg19: chr1-62950858;