Variant 11-65557854-CCAGCAGCAGCAGCAGCAGCAG-CCAGCAGCAGCAG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001130144.3(LTBP3):c.97_105delCTGCTGCTG(p.Leu33_Leu35del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00459 in 1,320,212 control chromosomes in the GnomAD database, including 226 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.024 ( 163 hom., cov: 27)

Exomes 𝑓: 0.0021 ( 63 hom. )

Consequence

LTBP3
NM_001130144.3 conservative_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.541

Variant links:

Genes affected

LTBP3 (HGNC:6716): (latent transforming growth factor beta binding protein 3) The protein encoded by this gene forms a complex with transforming growth factor beta (TGF-beta) proteins and may be involved in their subcellular localization. Activation of this complex requires removal of the encoded binding protein. This protein also may play a structural role in the extracellular matrix. Three transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Jan 2010]

LTBP3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 11-65557854-CCAGCAGCAG-C is Benign according to our data. Variant chr11-65557854-CCAGCAGCAG-C is described in ClinVar as [Likely_benign]. Clinvar id is 464028.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr11-65557854-CCAGCAGCAG-C is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0808 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LTBP3	NM_001130144.3 linkuse as main transcript	c.97_105delCTGCTGCTG	p.Leu33_Leu35del	conservative_inframe_deletion	1/28	ENST00000301873.11	NP_001123616.1	Q9NS15-1Q8WYU6
LTBP3	NM_021070.4 linkuse as main transcript	c.97_105delCTGCTGCTG	p.Leu33_Leu35del	conservative_inframe_deletion	1/27		NP_066548.2	Q9NS15-2Q8WYU6
LTBP3	NM_001164266.1 linkuse as main transcript	c.-251_-243delCTGCTGCTG		5_prime_UTR_variant	1/27		NP_001157738.1	Q9NS15B9EG76Q8WYU6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LTBP3	ENST00000301873.11 linkuse as main transcript	c.97_105delCTGCTGCTG	p.Leu33_Leu35del	conservative_inframe_deletion	1/28	2	NM_001130144.3	ENSP00000301873.5		Q9NS15-1

Frequencies

GnomAD3 genomes

AF:

0.0242

AC:

3611

AN:

149144

Hom.:

162

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0834

Gnomad AMI

AF:

0.00330

Gnomad AMR

AF:

0.00805

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000195

Gnomad SAS

AF:

0.00167

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00325

Gnomad NFE

AF:

0.000553

Gnomad OTH

AF:

0.0147

GnomAD3 exomes

AF:

0.000454

AC:

AN:

33030

Hom.:

AF XY:

0.000209

AC XY:

AN XY:

19164

show subpopulations

Gnomad AFR exome

AF:

0.0175

Gnomad AMR exome

AF:

0.000304

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000321

Gnomad OTH exome

AF:

0.000977

GnomAD4 exome

AF:

0.00210

AC:

2454

AN:

1170978

Hom.:

AF XY:

0.00187

AC XY:

1070

AN XY:

572162

show subpopulations

Gnomad4 AFR exome

AF:

0.0765

Gnomad4 AMR exome

AF:

0.00271

Gnomad4 ASJ exome

AF:

0.0000565

Gnomad4 EAS exome

AF:

0.000236

Gnomad4 SAS exome

AF:

0.000521

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000339

Gnomad4 OTH exome

AF:

0.00429

GnomAD4 genome

AF:

0.0242

AC:

3609

AN:

149234

Hom.:

163

Cov.:

AF XY:

0.0236

AC XY:

1718

AN XY:

72838

show subpopulations

Gnomad4 AFR

AF:

0.0831

Gnomad4 AMR

AF:

0.00804

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.000196

Gnomad4 SAS

AF:

0.00167

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000553

Gnomad4 OTH

AF:

0.0146

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

Brachyolmia-amelogenesis imperfecta syndrome

Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

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Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

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