5-172333540-TA-T

Position:

• chr5-172333540-TA-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001017995.3(SH3PXD2B):​c.*4828del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.62 (28042 hom., cov: 0)
  • Exomes 𝑓: 0.59 (103085 hom.)
• Consequence: SH3PXD2B NM_001017995.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.198

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 5-172333540-TA-T is Benign according to our data. Variant chr5-172333540-TA-T is described in ClinVar as [Benign]. Clinvar id is 352725.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SH3PXD2B	NM_001017995.3	c.*4828del		3_prime_UTR_variant	13/13	ENST00000311601.6	NP_001017995.1
SH3PXD2B	XM_017009351.2	c.*4828del		3_prime_UTR_variant	14/14		XP_016864840.1
SH3PXD2B	NM_001308175.2	c.1189-8161del		intron_variant			NP_001295104.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH3PXD2B	ENST00000311601.6	c.*4828del		3_prime_UTR_variant	13/13	1	NM_001017995.3	ENSP00000309714	P1

Frequencies

GnomAD3 genomes AF: 0.616 AC: 91475 AN: 148584 Hom.: 28016 Cov.: 0

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.616

Gnomad AMR AF: 0.611

Gnomad ASJ AF: 0.688

Gnomad EAS AF: 0.637

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.656

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.609

GnomAD4 exome AF: 0.595 AC: 504733 AN: 848644 Hom.: 103085 Cov.: 0 AF XY: 0.597 AC XY: 243011 AN XY: 407334

Gnomad4 AFR exome AF: 0.516

Gnomad4 AMR exome AF: 0.572

Gnomad4 ASJ exome AF: 0.605

Gnomad4 EAS exome AF: 0.580

Gnomad4 SAS exome AF: 0.670

Gnomad4 FIN exome AF: 0.560

Gnomad4 NFE exome AF: 0.592

Gnomad4 OTH exome AF: 0.598

GnomAD4 genome AF: 0.616 AC: 91552 AN: 148692 Hom.: 28042 Cov.: 0 AF XY: 0.617 AC XY: 44670 AN XY: 72426

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.611

Gnomad4 ASJ AF: 0.688

Gnomad4 EAS AF: 0.638

Gnomad4 SAS AF: 0.808

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.608

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Frank-Ter Haar syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs35951290; hg19: chr5-171760544;