chr3-9360377-C-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_024453843.2(SRGAP3):c.-522+2463G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,152 control chromosomes in the GnomAD database, including 39,746 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.72 ( 39746 hom., cov: 33)
Consequence
SRGAP3
XM_024453843.2 intron
XM_024453843.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.546
Genes affected
SRGAP3 (HGNC:19744): (SLIT-ROBO Rho GTPase activating protein 3) Predicted to enable GTPase activator activity. Predicted to be involved in negative regulation of cell migration. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.962 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SRGAP3 | XM_024453843.2 | c.-522+2463G>T | intron_variant | XP_024309611.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
THUMPD3-AS1 | ENST00000468186.5 | n.2876-10311G>T | intron_variant | 1 | ||||||
ENSG00000254485 | ENST00000466431.6 | n.102+2463G>T | intron_variant | 2 | ||||||
SRGAP3 | ENST00000490889.2 | n.214+2463G>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.718 AC: 109163AN: 152034Hom.: 39716 Cov.: 33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.718 AC: 109247AN: 152152Hom.: 39746 Cov.: 33 AF XY: 0.728 AC XY: 54184AN XY: 74382
GnomAD4 genome
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at