rs11704314
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_015705.6(SGSM3):c.91-210A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,264 control chromosomes in the GnomAD database, including 1,806 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 0.14 ( 1806 hom., cov: 33)
Consequence
SGSM3
NM_015705.6 intron
NM_015705.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.02
Genes affected
SGSM3 (HGNC:25228): (small G protein signaling modulator 3) Enables GTPase activator activity and small GTPase binding activity. Involved in several processes, including Rap protein signal transduction; positive regulation of GTPase activity; and regulation of Rab protein signal transduction. Located in 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=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.279 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SGSM3 | NM_015705.6 | c.91-210A>G | intron_variant | ENST00000248929.14 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SGSM3 | ENST00000248929.14 | c.91-210A>G | intron_variant | 1 | NM_015705.6 | P1 | |||
SGSM3 | ENST00000457767.5 | c.-111-210A>G | intron_variant | 2 | |||||
SGSM3 | ENST00000485962.5 | n.252-210A>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.137 AC: 20895AN: 152146Hom.: 1804 Cov.: 33
GnomAD3 genomes
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152146
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33
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.137 AC: 20894AN: 152264Hom.: 1806 Cov.: 33 AF XY: 0.135 AC XY: 10055AN XY: 74460
GnomAD4 genome
?
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20894
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33
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10055
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74460
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439
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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