rs2224451
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003026.5(SH3GL2):c.45+57469T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,230 control chromosomes in the GnomAD database, including 63,675 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 0.90 ( 63675 hom., cov: 32)
Consequence
SH3GL2
NM_003026.5 intron
NM_003026.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.266
Genes affected
SH3GL2 (HGNC:10831): (SH3 domain containing GRB2 like 2, endophilin A1) Enables identical protein binding activity. Involved in negative regulation of blood-brain barrier permeability; negative regulation of gene expression; and negative regulation of protein phosphorylation. Located in perinuclear region of 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=-0.68).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3GL2 | NM_003026.5 | c.45+57469T>A | intron_variant | ENST00000380607.5 | |||
SH3GL2 | XM_011518005.4 | c.147+18541T>A | intron_variant | ||||
SH3GL2 | XM_047423730.1 | c.-61+29502T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3GL2 | ENST00000380607.5 | c.45+57469T>A | intron_variant | 1 | NM_003026.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.904 AC: 137447AN: 152112Hom.: 63631 Cov.: 32
GnomAD3 genomes
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137447
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.904 AC: 137549AN: 152230Hom.: 63675 Cov.: 32 AF XY: 0.907 AC XY: 67492AN XY: 74436
GnomAD4 genome
?
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137549
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32
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67492
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74436
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3383
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at