1-17027878-GGAAGAAGAAGAA-GGAAGAAGAAGAAGAA
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP6BS1
The NM_003000.3(SDHB):c.424-16_424-14dupTTC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0008 in 1,377,890 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003000.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00118 AC: 179AN: 151550Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00127 AC: 284AN: 222768Hom.: 0 AF XY: 0.00128 AC XY: 154AN XY: 120738
GnomAD4 exome AF: 0.000752 AC: 922AN: 1226224Hom.: 0 Cov.: 16 AF XY: 0.000804 AC XY: 500AN XY: 622142
GnomAD4 genome AF: 0.00119 AC: 180AN: 151666Hom.: 1 Cov.: 32 AF XY: 0.00105 AC XY: 78AN XY: 74084
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:2
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Variant classified as Uncertain Significance - Favor Benign. The 424-16_424-14du pTTC variant in SDHB has not been previously identified by our laboratory or in the literature. This variant is located in the 3' splice region. Computational t ools do not suggest an impact to splicing. However, this information is not pred ictive enough to rule out pathogenicity. In summary, although this data supports that the 424-16_424-14dupTTC variant may be benign, additional studies are need ed to fully assess its clinical significance. -
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not provided Benign:3
SDHB: BP4, BS1 -
See Variant Classification Assertion Criteria. -
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Hereditary pheochromocytoma-paraganglioma Benign:2
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Pheochromocytoma Uncertain:1
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Carney-Stratakis syndrome Uncertain:1
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Pheochromocytoma;C0238198:Gastrointestinal stromal tumor;C1861848:Paragangliomas 4 Benign:1
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Gastrointestinal stromal tumor Benign:1
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Hereditary cancer-predisposing syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at