chr11-47358725-G-GCA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 4P and 10B. PVS1_StrongBP6_ModerateBA1
The ENST00000533968.1(SPI1):c.610_611dupTG(p.Met205AlafsTer24) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 940,472 control chromosomes in the GnomAD database, including 9,290 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000533968.1 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPI1 | ENST00000533968.1 | c.610_611dupTG | p.Met205AlafsTer24 | frameshift_variant | Exon 4 of 4 | 1 | ENSP00000438846.1 | |||
SPI1 | ENST00000378538.8 | c.493+117_493+118dupTG | intron_variant | Intron 4 of 4 | 1 | NM_003120.3 | ENSP00000367799.4 | |||
SPI1 | ENST00000227163.8 | c.496+117_496+118dupTG | intron_variant | Intron 4 of 4 | 2 | ENSP00000227163.4 | ||||
SPI1 | ENST00000533030.1 | c.46-3181_46-3180dupTG | intron_variant | Intron 1 of 1 | 2 | ENSP00000443865.1 |
Frequencies
GnomAD3 genomes AF: 0.219 AC: 32995AN: 150802Hom.: 4235 Cov.: 27
GnomAD3 exomes AF: 0.208 AC: 25255AN: 121646Hom.: 1381 AF XY: 0.199 AC XY: 13092AN XY: 65788
GnomAD4 exome AF: 0.150 AC: 118168AN: 789558Hom.: 5056 Cov.: 11 AF XY: 0.149 AC XY: 61260AN XY: 410274
GnomAD4 genome AF: 0.219 AC: 33004AN: 150914Hom.: 4234 Cov.: 27 AF XY: 0.225 AC XY: 16574AN XY: 73666
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 39% of patients studied by a panel of primary immunodeficiencies. Number of patients: 37. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at