rs10077897

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001017995.3(SH3PXD2B):​c.157-7031C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0657 in 152,254 control chromosomes in the GnomAD database, including 502 homozygotes. 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: 𝑓 0.066 ( 502 hom., cov: 33)

Consequence

SH3PXD2B
NM_001017995.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.807
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SH3PXD2BNM_001017995.3 linkuse as main transcriptc.157-7031C>T intron_variant ENST00000311601.6 NP_001017995.1 A1X283
SH3PXD2BNM_001308175.2 linkuse as main transcriptc.157-7031C>T intron_variant NP_001295104.1 G3V144
SH3PXD2BXM_017009351.2 linkuse as main transcriptc.157-7031C>T intron_variant XP_016864840.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SH3PXD2BENST00000311601.6 linkuse as main transcriptc.157-7031C>T intron_variant 1 NM_001017995.3 ENSP00000309714.5 A1X283
SH3PXD2BENST00000519643.5 linkuse as main transcriptc.157-7031C>T intron_variant 1 ENSP00000430890.1 G3V144
SH3PXD2BENST00000636523.1 linkuse as main transcriptc.112-7031C>T intron_variant 5 ENSP00000490082.1 A0A1B0GUF2

Frequencies

GnomAD3 genomes
AF:
0.0656
AC:
9982
AN:
152136
Hom.:
499
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.145
Gnomad AMI
AF:
0.0395
Gnomad AMR
AF:
0.0412
Gnomad ASJ
AF:
0.0671
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00952
Gnomad FIN
AF:
0.0302
Gnomad MID
AF:
0.0253
Gnomad NFE
AF:
0.0377
Gnomad OTH
AF:
0.0616
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0657
AC:
9998
AN:
152254
Hom.:
502
Cov.:
33
AF XY:
0.0617
AC XY:
4595
AN XY:
74444
show subpopulations
Gnomad4 AFR
AF:
0.145
Gnomad4 AMR
AF:
0.0410
Gnomad4 ASJ
AF:
0.0671
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00932
Gnomad4 FIN
AF:
0.0302
Gnomad4 NFE
AF:
0.0377
Gnomad4 OTH
AF:
0.0610
Alfa
AF:
0.0543
Hom.:
66
Bravo
AF:
0.0706
Asia WGS
AF:
0.0170
AC:
58
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
5.8
DANN
Benign
0.75

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

LitVar

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

Other links and lift over

dbSNP: rs10077897; hg19: chr5-171840387; API