chr10-102504236-G-T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_016169.4(SUFU):c.84G>T(p.Ser28=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,612,700 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 Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. S28S) has been classified as Likely benign.
Frequency
Consequence
NM_016169.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SUFU | NM_016169.4 | c.84G>T | p.Ser28= | synonymous_variant | 1/12 | ENST00000369902.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SUFU | ENST00000369902.8 | c.84G>T | p.Ser28= | synonymous_variant | 1/12 | 1 | NM_016169.4 | P1 | |
SUFU | ENST00000423559.2 | c.84G>T | p.Ser28= | synonymous_variant | 1/10 | 1 | |||
SUFU | ENST00000369899.6 | c.84G>T | p.Ser28= | synonymous_variant | 1/11 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151754Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000817 AC: 2AN: 244944Hom.: 0 AF XY: 0.0000150 AC XY: 2AN XY: 133696
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1460946Hom.: 0 Cov.: 54 AF XY: 0.00000550 AC XY: 4AN XY: 726794
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151754Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74096
ClinVar
Submissions by phenotype
Gorlin syndrome;C0025149:Medulloblastoma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 10, 2023 | - - |
Hereditary cancer-predisposing syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 08, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at