rs755475561
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP6BS1
The NM_003002.4(SDHD):c.314+20delA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000768 in 1,613,840 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_003002.4 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SDHD | NM_003002.4 | c.314+20delA | intron_variant | Intron 3 of 3 | ENST00000375549.8 | NP_002993.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000175 AC: 44AN: 251452Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135910
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461546Hom.: 0 Cov.: 31 AF XY: 0.0000688 AC XY: 50AN XY: 727106
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152294Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74470
ClinVar
Submissions by phenotype
not specified Benign:2
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 Uncertain:1
The c.314+20delA alteration is located in Intron 3 (E) of the SDHD gene. This alteration consists of a deletion of 1 nucleotides at nucleotide position c.31420 Intron 3 (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Pheochromocytoma;C1847319:Carney-Stratakis syndrome;C1868633:Paragangliomas with sensorineural hearing loss;CN166604:Cowden syndrome 3 Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at