rs10889635
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032291.4(SGIP1):c.11-15955G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,022 control chromosomes in the GnomAD database, including 33,981 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 0.66 ( 33981 hom., cov: 32)
Consequence
SGIP1
NM_032291.4 intron
NM_032291.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.59
Genes affected
SGIP1 (HGNC:25412): (SH3GL interacting endocytic adaptor 1) SGIP1 functions as an endocytic protein that affects signaling by receptors in neuronal systems involved in energy homeostasis via its interaction with endophilins (see SH3GL3; MIM 603362) (Trevaskis et al., 2005 [PubMed 15919751] and Uezu et al., 2007 [PubMed 17626015]).[supplied by OMIM, Mar 2008]
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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=-0.96).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGIP1 | NM_032291.4 | c.11-15955G>A | intron_variant | ENST00000371037.9 | |||
LOC124904196 | XR_007066156.1 | n.15707G>A | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGIP1 | ENST00000371037.9 | c.11-15955G>A | intron_variant | 1 | NM_032291.4 |
Frequencies
GnomAD3 genomes ? AF: 0.659 AC: 100030AN: 151904Hom.: 33939 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 genome ? AF: 0.659 AC: 100134AN: 152022Hom.: 33981 Cov.: 32 AF XY: 0.661 AC XY: 49136AN XY: 74316
GnomAD4 genome
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49136
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3237
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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