5-170034394-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_004946.3(DOCK2):c.3468-5C>T variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000327 in 1,613,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_004946.3 splice_region, splice_polypyrimidine_tract, intron
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 |
---|---|---|---|---|---|---|---|
DOCK2 | NM_004946.3 | c.3468-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000520908.7 | |||
DOCK2 | NR_156756.1 | n.3571-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DOCK2 | ENST00000520908.7 | c.3468-5C>T | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | NM_004946.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000159 AC: 40AN: 250998Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135660
GnomAD4 exome AF: 0.000339 AC: 496AN: 1461598Hom.: 0 Cov.: 29 AF XY: 0.000345 AC XY: 251AN XY: 727110
GnomAD4 genome AF: 0.000210 AC: 32AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.000161 AC XY: 12AN XY: 74470
ClinVar
Submissions by phenotype
DOCK2 deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at