1-17023973-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003000.3(SDHB):c.642G>A(p.Gln214=) variant causes a splice region, synonymous change. The variant allele was found at a frequency of 0.000000686 in 1,457,408 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_003000.3 splice_region, synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SDHB | NM_003000.3 | c.642G>A | p.Gln214= | splice_region_variant, synonymous_variant | 6/8 | ENST00000375499.8 | |
SDHB | NM_001407361.1 | c.588G>A | p.Gln196= | splice_region_variant, synonymous_variant | 6/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDHB | ENST00000375499.8 | c.642G>A | p.Gln214= | splice_region_variant, synonymous_variant | 6/8 | 1 | NM_003000.3 | P1 | |
SDHB | ENST00000491274.6 | c.600G>A | p.Gln200= | splice_region_variant, synonymous_variant | 6/8 | 5 | |||
SDHB | ENST00000463045.3 | c.471G>A | p.Gln157= | splice_region_variant, synonymous_variant | 6/8 | 3 | |||
SDHB | ENST00000485515.5 | n.576G>A | splice_region_variant, non_coding_transcript_exon_variant | 6/7 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.86e-7 AC: 1AN: 1457408Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 725284
GnomAD4 genome ? Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at