rs12414407
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_016169.4(SUFU):c.1365+19T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 1,609,952 control chromosomes in the GnomAD database, including 346,385 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_016169.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.683 AC: 103853AN: 152102Hom.: 35723 Cov.: 34
GnomAD3 exomes AF: 0.659 AC: 165628AN: 251454Hom.: 55054 AF XY: 0.662 AC XY: 89918AN XY: 135898
GnomAD4 exome AF: 0.651 AC: 949428AN: 1457730Hom.: 310627 Cov.: 33 AF XY: 0.654 AC XY: 474177AN XY: 725372
GnomAD4 genome AF: 0.683 AC: 103944AN: 152222Hom.: 35758 Cov.: 34 AF XY: 0.680 AC XY: 50603AN XY: 74434
ClinVar
Submissions by phenotype
not specified Benign:4
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not provided Benign:3
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Variant summary: The SUFU c.1365+19T>C variant involves the alteration of a non-conserved intronic nucleotide. Mutation taster predicts the variant to be neutral along with 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 80437/121368 control chromosomes (including 26892 homozygotes) at a frequency of 0.6627529, indicating the variant to be the ancestral allele and a common benign polymorphism. Taken together, this variant is classified as Benign. -
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Joubert syndrome 32 Benign:1
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Gorlin syndrome Benign:1
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Gorlin syndrome;C0025149:Medulloblastoma Benign:1
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Familial meningioma Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at