rs369557828
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBS1BS2
The NM_003073.5(SMARCB1):c.93+7C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000313 in 1,567,500 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_003073.5 splice_region, 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 |
---|---|---|---|---|---|---|---|
SMARCB1 | NM_003073.5 | c.93+7C>T | splice_region_variant, intron_variant | ENST00000644036.2 | |||
SMARCB1 | NM_001007468.3 | c.93+7C>T | splice_region_variant, intron_variant | ||||
SMARCB1 | NM_001317946.2 | c.93+7C>T | splice_region_variant, intron_variant | ||||
SMARCB1 | NM_001362877.2 | c.93+7C>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMARCB1 | ENST00000644036.2 | c.93+7C>T | splice_region_variant, intron_variant | NM_003073.5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000132 AC: 20AN: 151720Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000431 AC: 10AN: 231772Hom.: 0 AF XY: 0.0000158 AC XY: 2AN XY: 126946
GnomAD4 exome AF: 0.0000205 AC: 29AN: 1415676Hom.: 0 Cov.: 25 AF XY: 0.0000212 AC XY: 15AN XY: 706158
GnomAD4 genome ? AF: 0.000132 AC: 20AN: 151824Hom.: 0 Cov.: 33 AF XY: 0.0000943 AC XY: 7AN XY: 74230
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at