10-102504150-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_016169.4(SUFU):c.-3C>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 0.0000013 in 1,542,292 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_016169.4 5_prime_UTR
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUFU | ENST00000369902 | c.-3C>T | 5_prime_UTR_variant | Exon 1 of 12 | 1 | NM_016169.4 | ENSP00000358918.4 | |||
SUFU | ENST00000423559 | c.-3C>T | 5_prime_UTR_variant | Exon 1 of 10 | 1 | ENSP00000411597.2 | ||||
SUFU | ENST00000369899 | c.-3C>T | 5_prime_UTR_variant | Exon 1 of 11 | 1 | ENSP00000358915.2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152222Hom.: 0 Cov.: 33
GnomAD4 exome AF: 7.19e-7 AC: 1AN: 1389962Hom.: 0 Cov.: 31 AF XY: 0.00000146 AC XY: 1AN XY: 685714
GnomAD4 genome AF: 0.00000656 AC: 1AN: 152330Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74486
ClinVar
Submissions by phenotype
Hereditary cancer-predisposing syndrome Uncertain:1
The c.-3C>T variant is located in the 5' untranslated region (5’ UTR) of the SUFU gene. This variant results from a C to T substitution 3 bases upstream from the first translated codon. This nucleotide position is well conserved in available vertebrate species. Based on the available evidence, the clinical significance of this variant remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at