chr11-118339233-AGAG-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP6_ModerateBS1
The NM_000732.6(CD3D):c.451-9_451-7del 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 0.0000118 in 1,613,168 control chromosomes in the GnomAD database, with no homozygous occurrence. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000732.6 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD3D | NM_000732.6 | c.451-9_451-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000300692.9 | |||
CD3D | NM_001040651.2 | c.319-9_319-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD3D | ENST00000300692.9 | c.451-9_451-7del | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_000732.6 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152112Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251476Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135914
GnomAD4 exome AF: 0.00000753 AC: 11AN: 1461056Hom.: 0 AF XY: 0.00000413 AC XY: 3AN XY: 726916
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152112Hom.: 0 Cov.: 31 AF XY: 0.0000808 AC XY: 6AN XY: 74290
ClinVar
Submissions by phenotype
Immunodeficiency 19 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at