chr10-102593638-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_016169.4(SUFU):c.600C>T(p.Ile200Ile) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00177 in 1,614,112 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_016169.4 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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SUFU | ENST00000369902.8 | c.600C>T | p.Ile200Ile | splice_region_variant, synonymous_variant | Exon 5 of 12 | 1 | NM_016169.4 | ENSP00000358918.4 | ||
SUFU | ENST00000423559.2 | c.600C>T | p.Ile200Ile | splice_region_variant, synonymous_variant | Exon 5 of 10 | 1 | ENSP00000411597.2 | |||
SUFU | ENST00000369899.6 | c.600C>T | p.Ile200Ile | splice_region_variant, synonymous_variant | Exon 5 of 11 | 1 | ENSP00000358915.2 | |||
SUFU | ENST00000471000.1 | n.382C>T | splice_region_variant, non_coding_transcript_exon_variant | Exon 3 of 6 | 5 |
Frequencies
GnomAD3 genomes AF: 0.00121 AC: 184AN: 152142Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00131 AC: 329AN: 251436Hom.: 1 AF XY: 0.00143 AC XY: 195AN XY: 135904
GnomAD4 exome AF: 0.00183 AC: 2671AN: 1461852Hom.: 1 Cov.: 31 AF XY: 0.00179 AC XY: 1302AN XY: 727232
GnomAD4 genome AF: 0.00120 AC: 182AN: 152260Hom.: 2 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74466
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:6
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SUFU: BP4, BP7 -
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not specified Benign:3
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This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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Hereditary cancer-predisposing syndrome Benign:2
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. -
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Gorlin syndrome;C0025149:Medulloblastoma Benign:1
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Familial meningioma Benign:1
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Medulloblastoma Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at