11-47359042-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_003120.3(SPI1):c.331-36C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.555 in 1,506,956 control chromosomes in the GnomAD database, including 240,438 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_003120.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPI1 | ENST00000378538.8 | c.331-36C>T | intron_variant | Intron 3 of 4 | 1 | NM_003120.3 | ENSP00000367799.4 | |||
SPI1 | ENST00000533968.1 | c.331-36C>T | intron_variant | Intron 3 of 3 | 1 | ENSP00000438846.1 | ||||
SPI1 | ENST00000227163.8 | c.334-36C>T | intron_variant | Intron 3 of 4 | 2 | ENSP00000227163.4 | ||||
SPI1 | ENST00000533030.1 | c.46-3496C>T | intron_variant | Intron 1 of 1 | 2 | ENSP00000443865.1 |
Frequencies
GnomAD3 genomes AF: 0.448 AC: 68076AN: 151938Hom.: 18101 Cov.: 32
GnomAD3 exomes AF: 0.516 AC: 77585AN: 150388Hom.: 21131 AF XY: 0.530 AC XY: 41933AN XY: 79054
GnomAD4 exome AF: 0.567 AC: 768422AN: 1354900Hom.: 222333 Cov.: 38 AF XY: 0.569 AC XY: 377000AN XY: 662542
GnomAD4 genome AF: 0.448 AC: 68086AN: 152056Hom.: 18105 Cov.: 32 AF XY: 0.445 AC XY: 33087AN XY: 74320
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 81% of patients studied by a panel of primary immunodeficiencies. Number of patients: 77. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at