NM_003073.5:c.-3G>T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_003073.5(SMARCB1):c.-3G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000686 in 1,602,478 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003073.5 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SMARCB1 | NM_003073.5 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 9 | ENST00000644036.2 | NP_003064.2 | ||
SMARCB1 | NM_001362877.2 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 9 | NP_001349806.1 | |||
SMARCB1 | NM_001317946.2 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 9 | NP_001304875.1 | |||
SMARCB1 | NM_001007468.3 | c.-3G>T | 5_prime_UTR_variant | Exon 1 of 9 | NP_001007469.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152092Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.00000689 AC: 10AN: 1450386Hom.: 0 Cov.: 29 AF XY: 0.00000969 AC XY: 7AN XY: 722088
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152092Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
The c.-3G>T variant is located in the 5' untranslated region (5’ UTR) of the SMARCB1 gene. This variant results from a G to T substitution 3 nucleotides upstream from the first translated codon. This variant has been detected in multiple individuals with no reported features of SMARCB1-related Coffin-Siris syndrome (Ambry internal data). This nucleotide position is well conserved in available vertebrate species. Based on the supporting evidence, the association of this alteration with SMARCB1-related tumor predisposition syndrome is unknown; however, the association of this alteration with SMARCB1-related Coffin-Siris syndrome is unlikely. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at