rs147554257
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020812.4(DOCK6):c.4205C>T(p.Thr1402Met) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000713 in 1,613,746 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_020812.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DOCK6 | ENST00000294618.12 | c.4205C>T | p.Thr1402Met | missense_variant, splice_region_variant | Exon 34 of 48 | 1 | NM_020812.4 | ENSP00000294618.6 | ||
DOCK6 | ENST00000587656.6 | c.4310C>T | p.Thr1437Met | missense_variant, splice_region_variant | Exon 35 of 49 | 5 | ENSP00000468638.2 | |||
ENSG00000267082 | ENST00000588634.1 | n.538-1729G>A | intron_variant | Intron 2 of 2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00378 AC: 575AN: 152164Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00100 AC: 249AN: 249106Hom.: 3 AF XY: 0.000762 AC XY: 103AN XY: 135174
GnomAD4 exome AF: 0.000393 AC: 574AN: 1461464Hom.: 6 Cov.: 34 AF XY: 0.000354 AC XY: 257AN XY: 726986
GnomAD4 genome AF: 0.00379 AC: 577AN: 152282Hom.: 3 Cov.: 32 AF XY: 0.00357 AC XY: 266AN XY: 74446
ClinVar
Submissions by phenotype
not provided Benign:6
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DOCK6: BS1, BS2 -
not specified Benign:1
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DOCK6-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at