9-127824342-C-T

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4_ModerateBP6

The NM_001114753.3(ENG):​c.1096G>A​(p.Asp366Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,870 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D366H) has been classified as Benign.

Frequency

Genomes: not found (cov: 30)
Exomes 𝑓: 0.0000027 ( 0 hom. )

Consequence

ENG
NM_001114753.3 missense

Scores

6
13

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:1

Conservation

PhyloP100: 1.23
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 Likely_benign. Variant got -1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.25109106).
BP6
Variant 9-127824342-C-T is Benign according to our data. Variant chr9-127824342-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1356315.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ENGNM_001114753.3 linkc.1096G>A p.Asp366Asn missense_variant Exon 8 of 15 ENST00000373203.9 NP_001108225.1 P17813-1Q96CG0A0A024R878
ENGNM_000118.4 linkc.1096G>A p.Asp366Asn missense_variant Exon 8 of 14 NP_000109.1 P17813-2Q5T9B9
ENGNM_001278138.2 linkc.550G>A p.Asp184Asn missense_variant Exon 8 of 15 NP_001265067.1 P17813Q96CG0F5GX88B7Z6Y5
ENGNM_001406715.1 linkc.1096G>A p.Asp366Asn missense_variant Exon 8 of 8 NP_001393644.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENGENST00000373203.9 linkc.1096G>A p.Asp366Asn missense_variant Exon 8 of 15 1 NM_001114753.3 ENSP00000362299.4 P17813-1
ENGENST00000344849.4 linkc.1096G>A p.Asp366Asn missense_variant Exon 8 of 14 1 ENSP00000341917.3 P17813-2
ENGENST00000480266.6 linkc.550G>A p.Asp184Asn missense_variant Exon 8 of 15 2 ENSP00000479015.1 F5GX88
ENGENST00000486329.1 linkn.64G>A non_coding_transcript_exon_variant Exon 1 of 3 2

Frequencies

GnomAD3 genomes
Cov.:
30
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251480
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135918
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
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:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000274
AC:
4
AN:
1461870
Hom.:
0
Cov.:
33
AF XY:
0.00000138
AC XY:
1
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000270
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
30
ExAC
AF:
0.00000824
AC:
1

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Telangiectasia, hereditary hemorrhagic, type 1 Uncertain:1
Feb 06, 2024
Fulgent Genetics, Fulgent Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Hereditary hemorrhagic telangiectasia Benign:1
Sep 06, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.099
BayesDel_addAF
Benign
-0.12
T
BayesDel_noAF
Benign
-0.40
CADD
Benign
17
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.63
D;T;.
Eigen
Benign
-0.20
Eigen_PC
Benign
-0.38
FATHMM_MKL
Benign
0.094
N
LIST_S2
Benign
0.76
T;T;T
M_CAP
Uncertain
0.13
D
MetaRNN
Benign
0.25
T;T;T
MetaSVM
Benign
-0.35
T
MutationAssessor
Uncertain
2.1
M;.;M
PrimateAI
Benign
0.39
T
PROVEAN
Benign
-1.9
N;.;N
REVEL
Benign
0.22
Sift
Uncertain
0.027
D;.;D
Sift4G
Uncertain
0.011
D;D;D
Polyphen
0.99
D;.;.
Vest4
0.22
MutPred
0.36
Loss of ubiquitination at K362 (P = 0.1179);.;Loss of ubiquitination at K362 (P = 0.1179);
MVP
0.82
MPC
0.75
ClinPred
0.88
D
GERP RS
3.6
Varity_R
0.18
gMVP
0.86

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.

Other links and lift over

dbSNP: rs1800956; hg19: chr9-130586621; API