rs1085307434

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5

The NM_001114753.3(ENG):​c.1742-22T>C variant causes a 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. Variant has been reported in ClinVar as Pathogenic (no stars). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: not found (cov: 33)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ENG
NM_001114753.3 intron

Scores

2

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 2.40
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 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 9-127816075-A-G is Pathogenic according to our data. Variant chr9-127816075-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 426045.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ENGNM_001114753.3 linkuse as main transcriptc.1742-22T>C intron_variant ENST00000373203.9 NP_001108225.1 P17813-1Q96CG0A0A024R878
ENGNM_000118.4 linkuse as main transcriptc.1742-22T>C intron_variant NP_000109.1 P17813-2Q5T9B9
ENGNM_001278138.2 linkuse as main transcriptc.1196-22T>C intron_variant NP_001265067.1 P17813Q96CG0F5GX88B7Z6Y5
LOC102723566NR_136302.1 linkuse as main transcriptn.10A>G non_coding_transcript_exon_variant 1/6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ENGENST00000373203.9 linkuse as main transcriptc.1742-22T>C intron_variant 1 NM_001114753.3 ENSP00000362299.4 P17813-1
ENGENST00000344849.4 linkuse as main transcriptc.1742-22T>C intron_variant 1 ENSP00000341917.3 P17813-2
ENGENST00000480266.6 linkuse as main transcriptc.1196-22T>C intron_variant 2 ENSP00000479015.1 F5GX88
ENSG00000225032ENST00000439298.5 linkuse as main transcriptn.10A>G non_coding_transcript_exon_variant 1/62

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1451562
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
721396
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Pulmonary arterial hypertension related to hereditary hemorrhagic telangiectasia Pathogenic:1
Pathogenic, no assertion criteria providedliterature onlyRare Disease Genomics Group, St George's University of London-- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.55
CADD
Benign
15
DANN
Benign
0.77
BranchPoint Hunter
6.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
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.

Other links and lift over

dbSNP: rs1085307434; hg19: chr9-130578354; API