rs9308932

Positions:

• chr2-33196832-C-A
• chr2-33196832-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206943.4(LTBP1):​c.1701+7981C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0807 in 152,006 control chromosomes in the GnomAD database, including 1,062 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 0.081 (1062 hom., cov: 32)
• Consequence: LTBP1 NM_206943.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03

Genes affected

LTBP1 (HGNC:6714): (latent transforming growth factor beta binding protein 1) The protein encoded by this gene belongs to the family of latent TGF-beta binding proteins (LTBPs). The secretion and activation of TGF-betas is regulated by their association with latency-associated proteins and with latent TGF-beta binding proteins. The product of this gene targets latent complexes of transforming growth factor beta to the extracellular matrix, where the latent cytokine is subsequently activated by several different mechanisms. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.217 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LTBP1	NM_206943.4	c.1701+7981C>A		intron_variant		ENST00000404816.7	NP_996826.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LTBP1	ENST00000404816.7	c.1701+7981C>A		intron_variant		5	NM_206943.4	ENSP00000386043	P3

Frequencies

GnomAD3 genomes AF: 0.0805 AC: 12221 AN: 151888 Hom.: 1051 Cov.: 32

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.0340

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.00726

Gnomad FIN AF: 0.0168

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0247

Gnomad OTH AF: 0.0668

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0807 AC: 12261 AN: 152006 Hom.: 1062 Cov.: 32 AF XY: 0.0773 AC XY: 5745 AN XY: 74310

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.0267

Gnomad4 SAS AF: 0.00748

Gnomad4 FIN AF: 0.0168

Gnomad4 NFE AF: 0.0247

Gnomad4 OTH AF: 0.0657

Alfa AF: 0.0461 Hom.: 86

Bravo AF: 0.0908

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.6
DANN	Benign	0.38

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: rs9308932; hg19: chr2-33421899;