3-33132664-T-G

Variant names:

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_006371.5(CRTAP):c.1032T>G(p.Thr344Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.405 in 1,612,246 control chromosomes in the GnomAD database, including 137,016 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.36 ( 10569 hom., cov: 32)

Exomes 𝑓: 0.41 ( 126447 hom. )

Consequence

CRTAP
NM_006371.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 0.869

Variant links:

Genes affected

CRTAP (HGNC:2379): (cartilage associated protein) The protein encoded by this gene is similar to the chicken and mouse CRTAP genes. The encoded protein is a scaffolding protein that may influence the activity of at least one member of the cytohesin/ARNO family in response to specific cellular stimuli. Defects in this gene are associated with osteogenesis imperfecta, a connective tissue disorder characterized by bone fragility and low bone mass. [provided by RefSeq, Jul 2008]

CRTAP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.55).

BP6

Variant 3-33132664-T-G is Benign according to our data. Variant chr3-33132664-T-G is described in ClinVar as [Benign]. Clinvar id is 259968.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr3-33132664-T-G is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=0.869 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CRTAP	NM_006371.5 link	c.1032T>G	p.Thr344Thr	synonymous_variant	Exon 5 of 7	ENST00000320954.11	NP_006362.1	O75718
CRTAP	NM_001393363.1 link	c.1032T>G	p.Thr344Thr	synonymous_variant	Exon 5 of 6		NP_001380292.1
CRTAP	NM_001393364.1 link	c.903T>G	p.Thr301Thr	synonymous_variant	Exon 4 of 6		NP_001380293.1
CRTAP	NM_001393365.1 link	c.882T>G	p.Thr294Thr	synonymous_variant	Exon 4 of 6		NP_001380294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CRTAP	ENST00000320954.11 link	c.1032T>G	p.Thr344Thr	synonymous_variant	Exon 5 of 7	1	NM_006371.5	ENSP00000323696.5	O75718
CRTAP	ENST00000449224.1 link	c.903T>G	p.Thr301Thr	synonymous_variant	Exon 4 of 6	2		ENSP00000409997.1	C9JP16
CRTAP	ENST00000485310.1 link	n.*64T>G		downstream_gene_variant		4

Frequencies

GnomAD3 genomes

AF:

0.361

AC:

54827

AN:

152018

Hom.:

10571

Cov.:

show subpopulations

Gnomad AFR

AF:

0.261

Gnomad AMI

AF:

0.371

Gnomad AMR

AF:

0.305

Gnomad ASJ

AF:

0.526

Gnomad EAS

AF:

0.138

Gnomad SAS

AF:

0.381

Gnomad FIN

AF:

0.390

Gnomad MID

AF:

0.468

Gnomad NFE

AF:

0.435

Gnomad OTH

AF:

0.410

GnomAD3 exomes

AF:

0.369

AC:

92886

AN:

251482

Hom.:

18827

AF XY:

0.383

AC XY:

52024

AN XY:

135908

show subpopulations

Gnomad AFR exome

AF:

0.264

Gnomad AMR exome

AF:

0.208

Gnomad ASJ exome

AF:

0.536

Gnomad EAS exome

AF:

0.136

Gnomad SAS exome

AF:

0.413

Gnomad FIN exome

AF:

0.395

Gnomad NFE exome

AF:

0.438

Gnomad OTH exome

AF:

0.399

GnomAD4 exome

AF:

0.409

AC:

597804

AN:

1460110

Hom.:

126447

Cov.:

AF XY:

0.412

AC XY:

299317

AN XY:

726480

show subpopulations

Gnomad4 AFR exome

AF:

0.264

Gnomad4 AMR exome

AF:

0.219

Gnomad4 ASJ exome

AF:

0.532

Gnomad4 EAS exome

AF:

0.121

Gnomad4 SAS exome

AF:

0.413

Gnomad4 FIN exome

AF:

0.397

Gnomad4 NFE exome

AF:

0.429

Gnomad4 OTH exome

AF:

0.404

GnomAD4 genome

AF:

0.360

AC:

54829

AN:

152136

Hom.:

10569

Cov.:

AF XY:

0.358

AC XY:

26604

AN XY:

74364

show subpopulations

Gnomad4 AFR

AF:

0.261

Gnomad4 AMR

AF:

0.304

Gnomad4 ASJ

AF:

0.526

Gnomad4 EAS

AF:

0.138

Gnomad4 SAS

AF:

0.381

Gnomad4 FIN

AF:

0.390

Gnomad4 NFE

AF:

0.435

Gnomad4 OTH

AF:

0.406

Alfa

AF:

0.390

Hom.:

8782

Bravo

AF:

0.347

Asia WGS

AF:

0.243

AC:

848

AN:

3478

EpiCase

AF:

0.439

EpiControl

AF:

0.453

ClinVar

Significance: Benign

Submissions summary: Benign:9

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Osteogenesis imperfecta type 7

Benign:5

Nov 25, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 13, 2018

Illumina Laboratory Services, Illumina

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Feb 04, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 30, 2021

Genome-Nilou Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

not specified

Benign:3

Genome Diagnostics Laboratory, Amsterdam University Medical Center

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 03, 2016

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:1

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

5.0

DANN

Benign

0.36

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over