rs12389790
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003022.3(SH3BGRL):c.46-26498G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 110,278 control chromosomes in the GnomAD database, including 2,195 homozygotes. There are 7,272 hemizygotes in GnomAD. 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
Consequence
NM_003022.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BGRL | NM_003022.3 | c.46-26498G>A | intron_variant | ENST00000373212.6 | |||
SH3BGRL | XM_011531013.1 | c.231+13206G>A | intron_variant | ||||
SH3BGRL | XM_011531014.2 | c.156+13206G>A | intron_variant | ||||
SH3BGRL | XM_047442354.1 | c.156+13206G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BGRL | ENST00000373212.6 | c.46-26498G>A | intron_variant | 1 | NM_003022.3 | P1 | |||
SH3BGRL | ENST00000481106.5 | n.259-26498G>A | intron_variant, non_coding_transcript_variant | 1 | |||||
SH3BGRL | ENST00000463546.5 | n.92-26498G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.222 AC: 24508AN: 110249Hom.: 2196 Cov.: 22 AF XY: 0.222 AC XY: 7249AN XY: 32599
GnomAD4 genome ? AF: 0.222 AC: 24524AN: 110278Hom.: 2195 Cov.: 22 AF XY: 0.223 AC XY: 7272AN XY: 32638
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at