4-2818270-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_001145856.2(SH3BP2):c.47C>T(p.Ala16Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000197 in 1,013,914 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001145856.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SH3BP2 | NM_001122681.2 | c.-4-2344C>T | intron_variant | ENST00000503393.8 | NP_001116153.1 | |||
SH3BP2 | NM_001145856.2 | c.47C>T | p.Ala16Val | missense_variant | 1/13 | NP_001139328.1 | ||
SH3BP2 | NM_001145855.2 | c.81-2344C>T | intron_variant | NP_001139327.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000817 AC: 12AN: 146882Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000923 AC: 8AN: 866930Hom.: 0 Cov.: 28 AF XY: 0.00000744 AC XY: 3AN XY: 403244
GnomAD4 genome AF: 0.0000816 AC: 12AN: 146984Hom.: 0 Cov.: 32 AF XY: 0.0000699 AC XY: 5AN XY: 71552
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 31, 2024 | The c.47C>T (p.A16V) alteration is located in exon 1 (coding exon 1) of the SH3BP2 gene. This alteration results from a C to T substitution at nucleotide position 47, causing the alanine (A) at amino acid position 16 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
SH3BP2-related disorder Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 02, 2024 | The SH3BP2 c.47C>T variant is predicted to result in the amino acid substitution p.Ala16Val. To our knowledge, this variant has not been reported in the literature or in a large population database, indicating this variant is rare. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at