rs139409304
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2
The NM_001122681.2(SH3BP2):c.1386G>A(p.Thr462=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000682 in 1,612,896 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T462T) has been classified as Likely benign.
Frequency
Consequence
NM_001122681.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SH3BP2 | NM_001122681.2 | c.1386G>A | p.Thr462= | synonymous_variant | 10/13 | ENST00000503393.8 | |
SH3BP2 | NM_001145856.2 | c.1557G>A | p.Thr519= | synonymous_variant | 10/13 | ||
SH3BP2 | NM_001145855.2 | c.1470G>A | p.Thr490= | synonymous_variant | 10/13 | ||
SH3BP2 | NM_003023.4 | c.1386G>A | p.Thr462= | synonymous_variant | 10/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SH3BP2 | ENST00000503393.8 | c.1386G>A | p.Thr462= | synonymous_variant | 10/13 | 1 | NM_001122681.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000145 AC: 22AN: 152214Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000144 AC: 36AN: 250458Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135590
GnomAD4 exome AF: 0.0000602 AC: 88AN: 1460682Hom.: 1 Cov.: 32 AF XY: 0.0000853 AC XY: 62AN XY: 726676
GnomAD4 genome ? AF: 0.000145 AC: 22AN: 152214Hom.: 0 Cov.: 32 AF XY: 0.000188 AC XY: 14AN XY: 74362
ClinVar
Submissions by phenotype
Fibrous dysplasia of jaw Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at