rs243404
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003025.4(SH3GL1):c.45+15647C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,078 control chromosomes in the GnomAD database, including 6,413 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 0.27 ( 6413 hom., cov: 32)
Consequence
SH3GL1
NM_003025.4 intron
NM_003025.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.677
Genes affected
SH3GL1 (HGNC:10830): (SH3 domain containing GRB2 like 1, endophilin A2) This gene encodes a member of the endophilin family of Src homology 3 domain-containing proteins. The encoded protein is involved in endocytosis and may also play a role in the cell cycle. Overexpression of this gene may play a role in leukemogenesis, and the encoded protein has been implicated in acute myeloid leukemia as a fusion partner of the myeloid-lymphoid leukemia protein. Pseudogenes of this gene are located on the long arm of chromosomes 11 and 17. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jan 2011]
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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=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3GL1 | NM_003025.4 | c.45+15647C>T | intron_variant | ENST00000269886.7 | NP_003016.1 | |||
SH3GL1 | NM_001199943.2 | c.45+15647C>T | intron_variant | NP_001186872.1 | ||||
SH3GL1 | NM_001199944.2 | c.45+15647C>T | intron_variant | NP_001186873.1 | ||||
SH3GL1 | XM_047439222.1 | c.-61+5375C>T | intron_variant | XP_047295178.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SH3GL1 | ENST00000269886.7 | c.45+15647C>T | intron_variant | 1 | NM_003025.4 | ENSP00000269886.2 |
Frequencies
GnomAD3 genomes AF: 0.270 AC: 41088AN: 151960Hom.: 6400 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.270 AC: 41116AN: 152078Hom.: 6413 Cov.: 32 AF XY: 0.278 AC XY: 20673AN XY: 74340
GnomAD4 genome
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1551
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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