rs12130333

Variant names:

• chr1-62726106-C-T
• rs12130333
• ENST00000812372.1:n.201-21631C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000812372.1(DOCK7-DT):​n.201-21631C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,172 control chromosomes in the GnomAD database, including 2,186 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 0.16 (2186 hom., cov: 32)
• Consequence: DOCK7-DT ENST00000812372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0700
• Publications: 73 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DOCK7-DT	ENST00000812372.1	n.201-21631C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.161 AC: 24481 AN: 152054 Hom.: 2185 Cov.: 32

Gnomad AFR AF: 0.0975

Gnomad AMI AF: 0.203

Gnomad AMR AF: 0.207

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0119

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.204

Gnomad OTH AF: 0.145

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

GnomAD4 genome AF: 0.161 AC: 24485 AN: 152172 Hom.: 2186 Cov.: 32 AF XY: 0.161 AC XY: 11952 AN XY: 74404

African (AFR) AF: 0.0973 AC: 4042 AN: 41550

American (AMR) AF: 0.207 AC: 3170 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3470

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5188

South Asian (SAS) AF: 0.162 AC: 782 AN: 4820

European-Finnish (FIN) AF: 0.147 AC: 1553 AN: 10574

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.204 AC: 13856 AN: 67966

Other (OTH) AF: 0.144 AC: 304 AN: 2112

Alfa AF: 0.186 Hom.: 9465

Bravo AF: 0.163

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	11
DANN	Benign	0.59
PhyloP100		-0.070

Splicing

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

Other links and lift over

dbSNP: rs12130333; hg19: chr1-63191777;