chr3-122913022-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001031702.4(SEMA5B):c.2546C>G(p.Pro849Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000211 in 1,590,254 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001031702.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SEMA5B | NM_001031702.4 | c.2546C>G | p.Pro849Arg | missense_variant | 18/23 | ENST00000357599.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SEMA5B | ENST00000357599.8 | c.2546C>G | p.Pro849Arg | missense_variant | 18/23 | 1 | NM_001031702.4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000986 AC: 15AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000131 AC: 26AN: 198774Hom.: 0 AF XY: 0.000137 AC XY: 15AN XY: 109588
GnomAD4 exome AF: 0.000223 AC: 320AN: 1437998Hom.: 0 Cov.: 31 AF XY: 0.000224 AC XY: 160AN XY: 713414
GnomAD4 genome ? AF: 0.0000985 AC: 15AN: 152256Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74452
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 03, 2022 | The c.2546C>G (p.P849R) alteration is located in exon 18 (coding exon 17) of the SEMA5B gene. This alteration results from a C to G substitution at nucleotide position 2546, causing the proline (P) at amino acid position 849 to be replaced by an arginine (R). 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