9-89325591-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_024077.5(SECISBP2):c.347C>A(p.Pro116His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,832 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 Uncertain significance (★).
Frequency
Consequence
NM_024077.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SECISBP2 | NM_024077.5 | c.347C>A | p.Pro116His | missense_variant | 3/17 | ENST00000375807.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SECISBP2 | ENST00000375807.8 | c.347C>A | p.Pro116His | missense_variant | 3/17 | 1 | NM_024077.5 | P2 | |
SECISBP2 | ENST00000339901.8 | c.128C>A | p.Pro43His | missense_variant | 3/17 | 1 | A2 | ||
SECISBP2 | ENST00000470305.1 | n.3392C>A | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
SECISBP2 | ENST00000534113.6 | c.143C>A | p.Pro48His | missense_variant | 3/17 | 2 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461832Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727218
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2022 | The c.347C>A (p.P116H) alteration is located in exon 3 (coding exon 3) of the SECISBP2 gene. This alteration results from a C to A substitution at nucleotide position 347, causing the proline (P) at amino acid position 116 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.