rs2569232

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001017995.3(SH3PXD2B):​c.563-11T>G variant causes a intron 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

SH3PXD2B
NM_001017995.3 intron

Scores

2
Splicing: ADA: 0.0002623
2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.549
Variant links:
Genes affected
SH3PXD2B (HGNC:29242): (SH3 and PX domains 2B) This gene encodes an adapter protein that is characterized by a PX domain and four Src homology 3 domains. The encoded protein is required for podosome formation and is involved in cell adhesion and migration of numerous cell types. Mutations in this gene are the cause of Frank-ter Haar syndrome (FTHS), and also Borrone Dermato-Cardio-Skeletal (BDCS) syndrome. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2015]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SH3PXD2BNM_001017995.3 linkuse as main transcriptc.563-11T>G intron_variant ENST00000311601.6 NP_001017995.1 A1X283
SH3PXD2BNM_001308175.2 linkuse as main transcriptc.563-11T>G intron_variant NP_001295104.1 G3V144
SH3PXD2BXM_017009351.2 linkuse as main transcriptc.563-11T>G intron_variant XP_016864840.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SH3PXD2BENST00000311601.6 linkuse as main transcriptc.563-11T>G intron_variant 1 NM_001017995.3 ENSP00000309714.5 A1X283
SH3PXD2BENST00000519643.5 linkuse as main transcriptc.563-11T>G intron_variant 1 ENSP00000430890.1 G3V144
SH3PXD2BENST00000636523.1 linkuse as main transcriptc.518-11T>G intron_variant 5 ENSP00000490082.1 A0A1B0GUF2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
37
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.33
DANN
Benign
0.52

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00026
dbscSNV1_RF
Benign
0.078
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2569232; hg19: chr5-171785892; API