rs1280482569
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PVS1_ModeratePM2PP5_Moderate
The NM_020812.4(DOCK6):c.4650+1_4650+3del variant causes a splice donor, splice donor region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152,068 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★).
Frequency
Consequence
NM_020812.4 splice_donor, splice_donor_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DOCK6 | NM_020812.4 | c.4650+1_4650+3del | splice_donor_variant, splice_donor_region_variant, intron_variant | ENST00000294618.12 | NP_065863.2 | |||
LOC105372273 | NR_134909.1 | n.538-4146_538-4144del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DOCK6 | ENST00000294618.12 | c.4650+1_4650+3del | splice_donor_variant, splice_donor_region_variant, intron_variant | 1 | NM_020812.4 | ENSP00000294618 | A2 | |||
ENST00000588634.1 | n.538-4146_538-4144del | intron_variant, non_coding_transcript_variant | 4 | |||||||
DOCK6 | ENST00000587656.6 | c.4755+1_4755+3del | splice_donor_variant, splice_donor_region_variant, intron_variant | 5 | ENSP00000468638 | P3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 31
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2017 | Lines of evidence used in support of classification: POSITIVE: Relevant Alteration(s) Detected - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at