chr3-15256165-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004844.5(SH3BP5):c.1289G>A(p.Arg430Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000291 in 1,614,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004844.5 missense
Scores
Clinical Significance
Conservation
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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.1289G>A | p.Arg430Gln | missense_variant | 9/9 | ENST00000383791.8 | |
SH3BP5-AS1 | NR_046084.1 | n.1982C>T | non_coding_transcript_exon_variant | 1/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP5 | ENST00000383791.8 | c.1289G>A | p.Arg430Gln | missense_variant | 9/9 | 1 | NM_004844.5 | P1 | |
SH3BP5-AS1 | ENST00000420195.1 | n.1982C>T | non_coding_transcript_exon_variant | 1/3 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152176Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249688Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135124
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727246
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74460
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at