1-167431751-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_198053.3(CD247):c.430-5G>A 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 0.000044 in 1,613,604 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_198053.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD247 | NM_198053.3 | c.430-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000362089.10 | NP_932170.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD247 | ENST00000362089.10 | c.430-5G>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_198053.3 | ENSP00000354782 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151962Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000762 AC: 19AN: 249294Hom.: 0 AF XY: 0.0000593 AC XY: 8AN XY: 134948
GnomAD4 exome AF: 0.0000472 AC: 69AN: 1461642Hom.: 0 Cov.: 30 AF XY: 0.0000564 AC XY: 41AN XY: 727150
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151962Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74204
ClinVar
Submissions by phenotype
Immunodeficiency 25 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jun 03, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at