chr2-86785979-A-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001768.7(CD8A):c.657-8T>C variant causes a splice region, splice polypyrimidine tract, intron change. The variant allele was found at a frequency of 0.0000211 in 1,613,036 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_001768.7 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 |
---|---|---|---|---|---|---|---|
CD8A | NM_001768.7 | c.657-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000283635.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD8A | ENST00000283635.8 | c.657-8T>C | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001768.7 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000112 AC: 17AN: 152210Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249168Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134882
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460826Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 726840
GnomAD4 genome ? AF: 0.000112 AC: 17AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74356
ClinVar
Submissions by phenotype
Susceptibility to respiratory infections associated with CD8alpha chain mutation Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 25, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at