chr3-15256246-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004844.5(SH3BP5):āc.1208G>Cā(p.Gly403Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,614,200 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004844.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP5 | NM_004844.5 | c.1208G>C | p.Gly403Ala | missense_variant | 9/9 | ENST00000383791.8 | |
SH3BP5-AS1 | NR_046084.1 | n.2063C>G | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP5 | ENST00000383791.8 | c.1208G>C | p.Gly403Ala | missense_variant | 9/9 | 1 | NM_004844.5 | P1 | |
SH3BP5-AS1 | ENST00000420195.1 | n.2063C>G | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000112 AC: 17AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000442 AC: 11AN: 249122Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 134858
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1461890Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 727248
GnomAD4 genome AF: 0.000125 AC: 19AN: 152310Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 12AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.1208G>C (p.G403A) alteration is located in exon 9 (coding exon 9) of the SH3BP5 gene. This alteration results from a G to C substitution at nucleotide position 1208, causing the glycine (G) at amino acid position 403 to be replaced by an alanine (A). 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