chr1-161356863-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_003001.5(SDHC):c.405+23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000148 in 1,610,248 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003001.5 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHC | NM_003001.5 | c.405+23C>T | intron_variant | Intron 5 of 5 | ENST00000367975.7 | NP_002992.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000257 AC: 39AN: 152012Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000249 AC: 62AN: 249024Hom.: 0 AF XY: 0.000274 AC XY: 37AN XY: 134798
GnomAD4 exome AF: 0.000137 AC: 200AN: 1458122Hom.: 0 Cov.: 30 AF XY: 0.000153 AC XY: 111AN XY: 725592
GnomAD4 genome AF: 0.000256 AC: 39AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.000363 AC XY: 27AN XY: 74350
ClinVar
Submissions by phenotype
not specified Uncertain:1Benign:1
Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Outside ROI; reported in 1 study as "pathogenicity to be confirmed" -
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Gastrointestinal stromal tumor;C1854336:Paragangliomas 3 Benign:1
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not provided Benign:1
This variant is associated with the following publications: (PMID: 22136840) -
Paragangliomas 3 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