chr10-102592664-G-A
Variant summary
Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_016169.4(SUFU):c.537G>A(p.Leu179Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000688 in 1,614,106 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 (★★).
Frequency
Consequence
NM_016169.4 synonymous
Scores
Clinical Significance
Conservation
Publications
- medulloblastomaInheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
- nevoid basal cell carcinoma syndromeInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Illumina, Genomics England PanelApp
- basal cell nevus syndrome 2Inheritance: AD Classification: STRONG Submitted by: G2P
- ocular motor apraxia, Cogan typeInheritance: AD Classification: STRONG Submitted by: Franklin by Genoox
- Joubert syndrome 32Inheritance: AR Classification: STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Ambry Genetics
- Joubert syndromeInheritance: AR, AD Classification: MODERATE, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics
- apraxiaInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
- ciliopathyInheritance: AR Classification: LIMITED Submitted by: ClinGen
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ACMG classification
Our verdict: Benign. The variant received -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SUFU | ENST00000369902.8 | c.537G>A | p.Leu179Leu | synonymous_variant | Exon 4 of 12 | 1 | NM_016169.4 | ENSP00000358918.4 | ||
SUFU | ENST00000423559.2 | c.537G>A | p.Leu179Leu | synonymous_variant | Exon 4 of 10 | 1 | ENSP00000411597.2 | |||
SUFU | ENST00000369899.6 | c.537G>A | p.Leu179Leu | synonymous_variant | Exon 4 of 11 | 1 | ENSP00000358915.2 | |||
SUFU | ENST00000471000.1 | n.319G>A | non_coding_transcript_exon_variant | Exon 2 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000398 AC: 10AN: 251394 AF XY: 0.0000368 show subpopulations
GnomAD4 exome AF: 0.0000718 AC: 105AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.0000633 AC XY: 46AN XY: 727240 show subpopulations
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152228Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74364 show subpopulations
ClinVar
Submissions by phenotype
Gorlin syndrome;C0025149:Medulloblastoma Benign:1
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not provided Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
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