3-15257081-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004844.5(SH3BP5):āc.922A>Gā(p.Ser308Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000929 in 1,614,192 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 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.922A>G | p.Ser308Gly | missense_variant | 8/9 | ENST00000383791.8 | |
SH3BP5-AS1 | NR_046084.1 | n.2898T>C | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP5 | ENST00000383791.8 | c.922A>G | p.Ser308Gly | missense_variant | 8/9 | 1 | NM_004844.5 | P1 | |
SH3BP5-AS1 | ENST00000420195.1 | n.2898T>C | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251334Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135824
GnomAD4 exome AF: 0.00000752 AC: 11AN: 1461884Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727244
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 31, 2024 | The c.922A>G (p.S308G) alteration is located in exon 8 (coding exon 8) of the SH3BP5 gene. This alteration results from a A to G substitution at nucleotide position 922, causing the serine (S) at amino acid position 308 to be replaced by a glycine (G). 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