chr19-11200312-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_020812.4(DOCK6):c.6097C>T(p.Leu2033Phe) variant causes a missense change. The variant allele was found at a frequency of 0.000107 in 1,563,594 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. L2033L) has been classified as Uncertain significance.
Frequency
Consequence
NM_020812.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DOCK6 | NM_020812.4 | c.6097C>T | p.Leu2033Phe | missense_variant | 47/48 | ENST00000294618.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK6 | ENST00000294618.12 | c.6097C>T | p.Leu2033Phe | missense_variant | 47/48 | 1 | NM_020812.4 | A2 | |
DOCK6 | ENST00000587656.6 | c.6202C>T | p.Leu2068Phe | missense_variant | 48/49 | 5 | P3 | ||
DOCK6 | ENST00000587734.1 | c.76-773C>T | intron_variant | 5 | |||||
DOCK6 | ENST00000586702.1 | n.1000C>T | non_coding_transcript_exon_variant | 6/7 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000250 AC: 43AN: 172336Hom.: 0 AF XY: 0.000227 AC XY: 21AN XY: 92382
GnomAD4 exome AF: 0.000108 AC: 152AN: 1411276Hom.: 1 Cov.: 32 AF XY: 0.000112 AC XY: 78AN XY: 697370
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152318Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 05, 2024 | - - |
Adams-Oliver syndrome 2 Other:1
not provided, no classification provided | phenotyping only | GenomeConnect, ClinGen | - | GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at