9-127843248-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP5_Moderate

The NM_001114753.3(ENG):​c.68-3C>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★).

Frequency

Genomes: not found (cov: 30)

Consequence

ENG
NM_001114753.3 splice_region, intron

Scores

2
Splicing: ADA: 0.9965
2

Clinical Significance

Pathogenic criteria provided, single submitter P:1

Conservation

PhyloP100: 1.48
Variant links:
Genes affected
ENG (HGNC:3349): (endoglin) This gene encodes a homodimeric transmembrane protein which is a major glycoprotein of the vascular endothelium. This protein is a component of the transforming growth factor beta receptor complex and it binds to the beta1 and beta3 peptides with high affinity. Mutations in this gene cause hereditary hemorrhagic telangiectasia, also known as Osler-Rendu-Weber syndrome 1, an autosomal dominant multisystemic vascular dysplasia. This gene may also be involved in preeclampsia and several types of cancer. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2013]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 4 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-127843248-G-C is Pathogenic according to our data. Variant chr9-127843248-G-C is described in ClinVar as [Pathogenic]. Clinvar id is 568333.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ENGNM_001114753.3 linkc.68-3C>G splice_region_variant, intron_variant ENST00000373203.9 NP_001108225.1 P17813-1Q96CG0A0A024R878
ENGNM_000118.4 linkc.68-3C>G splice_region_variant, intron_variant NP_000109.1 P17813-2Q5T9B9
ENGNM_001278138.2 linkc.-479-3C>G splice_region_variant, intron_variant NP_001265067.1 P17813Q96CG0F5GX88B7Z6Y5
ENGNM_001406715.1 linkc.68-3C>G splice_region_variant, intron_variant NP_001393644.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENGENST00000373203.9 linkc.68-3C>G splice_region_variant, intron_variant 1 NM_001114753.3 ENSP00000362299.4 P17813-1
ENGENST00000344849.4 linkc.68-3C>G splice_region_variant, intron_variant 1 ENSP00000341917.3 P17813-2
ENGENST00000480266.6 linkc.-479-3C>G splice_region_variant, intron_variant 2 ENSP00000479015.1 F5GX88

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD4 exome
Cov.:
32
GnomAD4 genome
Cov.:
30

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Hereditary hemorrhagic telangiectasia Pathogenic:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpAug 04, 2023For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with altered splicing resulting in skipping of exon 2 (PMID: 25970827). ClinVar contains an entry for this variant (Variation ID: 568333). This variant has been observed in individuals with ENG-related disease (PMID: 25970827; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 1 of the ENG gene. It does not directly change the encoded amino acid sequence of the ENG protein. It affects a nucleotide within the consensus splice site. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.56
CADD
Benign
20
DANN
Benign
0.79

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
1.0
dbscSNV1_RF
Pathogenic
0.89
SpliceAI score (max)
0.75
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.75
Position offset: -3

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: rs773334730; hg19: chr9-130605527; API