rs139719
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098497.3(SGSM1):c.1770+70T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.674 in 1,495,790 control chromosomes in the GnomAD database, including 340,819 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 0.68 ( 35017 hom., cov: 32)
Exomes 𝑓: 0.67 ( 305802 hom. )
Consequence
SGSM1
NM_001098497.3 intron
NM_001098497.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.804
Genes affected
SGSM1 (HGNC:29410): (small G protein signaling modulator 1) Enables GTPase activator activity and small GTPase binding activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Located in cytoplasmic vesicle membrane and cytosol. [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=-0.9).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGSM1 | NM_001098497.3 | c.1770+70T>C | intron_variant | ENST00000400358.9 | |||
SGSM1 | NM_001039948.4 | c.1935+70T>C | intron_variant | ||||
SGSM1 | NM_001098498.3 | c.1770+70T>C | intron_variant | ||||
SGSM1 | NM_133454.4 | c.1935+70T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGSM1 | ENST00000400358.9 | c.1770+70T>C | intron_variant | 1 | NM_001098497.3 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.678 AC: 103023AN: 152016Hom.: 34967 Cov.: 32
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GnomAD4 exome AF: 0.674 AC: 905129AN: 1343656Hom.: 305802 AF XY: 0.674 AC XY: 441985AN XY: 655752
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GnomAD4 genome ? AF: 0.678 AC: 103128AN: 152134Hom.: 35017 Cov.: 32 AF XY: 0.684 AC XY: 50834AN XY: 74370
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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