4-2827265-C-G

Variant names:

• chr4-2827265-C-G
• NM_001122681.2:c.464C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001122681.2(SH3BP2):​c.464C>G​(p.Ala155Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A155V) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: SH3BP2 NM_001122681.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.25

Genes affected

SH3BP2 (HGNC:10825): (SH3 domain binding protein 2) The protein encoded by this gene has an N-terminal pleckstrin homology (PH) domain, an SH3-binding proline-rich region, and a C-terminal SH2 domain. The protein binds to the SH3 domains of several proteins including the ABL1 and SYK protein tyrosine kinases , and functions as a cytoplasmic adaptor protein to positively regulate transcriptional activity in T, natural killer (NK), and basophilic cells. Mutations in this gene result in cherubism. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33969215).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3BP2	NM_001122681.2	c.464C>G	p.Ala155Gly	missense_variant	Exon 6 of 13	ENST00000503393.8	NP_001116153.1
SH3BP2	NM_001145856.2	c.635C>G	p.Ala212Gly	missense_variant	Exon 6 of 13		NP_001139328.1
SH3BP2	NM_001145855.2	c.548C>G	p.Ala183Gly	missense_variant	Exon 6 of 13		NP_001139327.1
SH3BP2	NM_003023.4	c.464C>G	p.Ala155Gly	missense_variant	Exon 6 of 13		NP_003014.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3BP2	ENST00000503393.8	c.464C>G	p.Ala155Gly	missense_variant	Exon 6 of 13	1	NM_001122681.2	ENSP00000422168.3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Benign	-0.037	T
BayesDel_noAF	Benign	-0.29
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.28	T;.;T;T;.;T;T;.;T
Eigen	Benign	-0.10
Eigen_PC	Benign	-0.16
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.96	.;D;D;D;D;.;.;D;D
M_CAP	Pathogenic	0.48	D
MetaRNN	Benign	0.34	T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.014	D
MutationAssessor	Benign	1.9	L;.;.;.;.;L;L;.;L
PrimateAI	Benign	0.38	T
PROVEAN	Benign	-1.1	N;N;N;N;N;N;N;N;N
REVEL	Benign	0.095
Sift	Uncertain	0.021	D;D;D;D;D;D;D;D;D
Sift4G	Benign	0.14	T;D;D;D;T;T;T;T;T
Polyphen		0.46	P;.;.;.;.;P;P;.;P
Vest4		0.28
MutPred		0.20		Loss of catalytic residue at A155 (P = 0.0592);Loss of catalytic residue at A155 (P = 0.0592);Loss of catalytic residue at A155 (P = 0.0592);Loss of catalytic residue at A155 (P = 0.0592);.;Loss of catalytic residue at A155 (P = 0.0592);Loss of catalytic residue at A155 (P = 0.0592);.;Loss of catalytic residue at A155 (P = 0.0592);
MVP		0.90
MPC		0.49
ClinPred		0.46	T
GERP RS		4.1
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Varity_R		0.070

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr4-2828992;