NM_001079.4:c.1289+10G>A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP6BS1
The NM_001079.4(ZAP70):c.1289+10G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000164 in 1,604,568 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001079.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ZAP70 | NM_001079.4 | c.1289+10G>A | intron_variant | Intron 10 of 13 | ENST00000264972.10 | NP_001070.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000848 AC: 129AN: 152126Hom.: 0 Cov.: 34
GnomAD3 exomes AF: 0.000233 AC: 57AN: 244248Hom.: 0 AF XY: 0.000233 AC XY: 31AN XY: 132806
GnomAD4 exome AF: 0.0000916 AC: 133AN: 1452324Hom.: 0 Cov.: 35 AF XY: 0.0000818 AC XY: 59AN XY: 721022
GnomAD4 genome AF: 0.000854 AC: 130AN: 152244Hom.: 0 Cov.: 34 AF XY: 0.000860 AC XY: 64AN XY: 74448
ClinVar
Submissions by phenotype
Combined immunodeficiency due to ZAP70 deficiency Uncertain:1
This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. -
not provided Uncertain:1
- -
ZAP70-Related Severe Combined Immunodeficiency Benign:1
- -
ZAP70-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at