1-62729989-C-T

Variant names:

• chr1-62729989-C-T
• rs6664692
• ENST00000812372.1:n.201-17748C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000812372.1(DOCK7-DT):​n.201-17748C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,126 control chromosomes in the GnomAD database, including 39,110 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 0.70 (39110 hom., cov: 33)
• Consequence: DOCK7-DT ENST00000812372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.530
• Publications: 5 publications found

Genes affected

DOCK7-DT (HGNC:55670): (DOCK7 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.802 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812372.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DOCK7-DT	ENST00000812372.1		n.201-17748C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.697 AC: 105897 AN: 152008 Hom.: 39109 Cov.: 33

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.763

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.800

Gnomad EAS AF: 0.789

Gnomad SAS AF: 0.664

Gnomad FIN AF: 0.788

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.808

Gnomad OTH AF: 0.745

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

GnomAD4 genome AF: 0.696 AC: 105919 AN: 152126 Hom.: 39110 Cov.: 33 AF XY: 0.699 AC XY: 52003 AN XY: 74384

African (AFR) AF: 0.428 AC: 17713 AN: 41422

American (AMR) AF: 0.808 AC: 12367 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.800 AC: 2778 AN: 3472

East Asian (EAS) AF: 0.789 AC: 4090 AN: 5184

South Asian (SAS) AF: 0.665 AC: 3203 AN: 4820

European-Finnish (FIN) AF: 0.788 AC: 8351 AN: 10592

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.808 AC: 54943 AN: 68016

Other (OTH) AF: 0.737 AC: 1557 AN: 2114

Alfa AF: 0.766 Hom.: 26866

Bravo AF: 0.689

Asia WGS AF: 0.661 AC: 2297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.61
DANN	Benign	0.67
PhyloP100		-0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6664692;

hg19: chr1-63195660;

COSMIC: COSV59947564;