7-100806419-C-T
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_ModeratePM2PP5_Very_Strong
The NM_004444.5(EPHB4):c.2484+1G>A variant causes a splice donor, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,444 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
EPHB4
NM_004444.5 splice_donor, intron
NM_004444.5 splice_donor, intron
Scores
5
1
1
Splicing: ADA: 1.000
2
Clinical Significance
Conservation
PhyloP100: 7.91
Genes affected
EPHB4 (HGNC:3395): (EPH receptor B4) Ephrin receptors and their ligands, the ephrins, mediate numerous developmental processes, particularly in the nervous system. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. The Eph family of receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Ephrin receptors make up the largest subgroup of the receptor tyrosine kinase (RTK) family. The protein encoded by this gene binds to ephrin-B2 and plays an essential role in vascular development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.050269905 fraction of the gene. Cryptic splice site detected, with MaxEntScore 4.4, offset of -48, new splice context is: gagGTgatg. Cryptic site results in inframe change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 7-100806419-C-T is Pathogenic according to our data. Variant chr7-100806419-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 590874.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr7-100806419-C-T is described in Lovd as [Likely_pathogenic].
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 249748Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134910
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460444Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 726498
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:5
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Capillary malformation-arteriovenous malformation 2 Pathogenic:3
| Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 21, 2018 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | Feb 02, 2022 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with capillary malformation-arteriovenous malformation 2 (MIM#618196). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMIDs: 29905864, 27400125, 30578106). (I) 0211 - Canonical splice site variant without proven consequence on splicing (no functional evidence available). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (1 heterozygote, 0 homozygotes). (SP) 0505 - Abnormal splicing is predicted by in silico tools and affected nucleotide is highly conserved. (SP) 0703 - Other splice variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. c.2484+1G>T was detected in an individual with vein of Galen aneurysm malformation and cutaneous capillary malformation, the variant was maternally inherited and mother also was found to have cutaneous capillary malformation; RT-PCR studies showed this variant results in an in-frame deletion p.(Met814_Val829del) (PMID: 29444212). In addition, the c.2484+2insT duplication that would impact the +3 nucleotide, has been identified in an individual with vein of Galen aneurysm malformation; it was determined to be paternally inherited, but the father was not available for a clinical evaluation (PMID: 29444212). (SP) 0803 - This variant has limited previous evidence of pathogenicity in unrelated individuals. It has been classified as pathogenic in ClinVar and detected in two individuals with capillary malformation-arteriovenous malformation 2 (PMID: 28687708, 30760892). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1205 - This variant has been shown to be maternally inherited (by segregation analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics, Royal Melbourne Hospital | Jun 26, 2020 | This sequence change affects the canonical donor splice site in intron 14 of EPHB4. It is expected to disrupt RNA splicing, but has not been confirmed with patient RNA studies. However, based on the assessment of another substitution at this position the variant likely results in the activation of an upstream cryptic donor site in exon 14 leading to an in-frame 16 amino acid deletion (p.Gly779_Asp828del; PMID: 29444212). The expected in-frame splicing aberration removes part of the tyrosine kinase domain, however it is unknown if this region is essential to function (PVS1_Moderate). The variant is present in a single individual in a large population cohort (PM2; rs927772349, 1/249,748 alleles in gnomAD v2.1). At least two individuals with capillary malformation-arteriovenous malformation (CV-AVM) have been identified with this variant (PS4_Supporting; PMID: 28687708, Royal Melbourne Hospital), and the phenotype was highly specific for EPHB4-related CV-AVM (PMID: 21348050), including the presence of Bier spots, telangiectasia, and epistaxis (PP4; Royal Melbourne Hospital). Based on the classification scheme RMH ACMG Guidelines v1.2.1, this variant is classified as LIKELY PATHOGENIC. Following criteria are met: PVS1_Moderate, PM2, PS4_Supporting, PP4. - |
not provided Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Mar 21, 2023 | The EPHB4 c.2484+1G>A variant (rs927772349), is reported in the literature in at least one individual affected with capillary malformation-arteriovenous malformation (Amyere 2017). This variant is reported in ClinVar (Variation ID: 590874). It is only observed on one allele in the Genome Aggregation Database, indicating it is not a common polymorphism. This variant disrupts the canonical splice donor site of intron 14, which is likely to disrupt gene function. Based on available information, the c.2484+1G>A variant is considered to be pathogenic. References: Amyere M et al. Germline Loss-of-Function Mutations in EPHB4 Cause a Second Form of Capillary Malformation-Arteriovenous Malformation (CM-AVM2) Deregulating RAS-MAPK Signaling. Circulation. 2017 Sep 12;136(11):1037-1048. PMID: 28687708. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 25, 2023 | In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 590874). Disruption of this splice site has been observed in individual(s) with clinical features of capillary malformation-arteriovenous malformation (PMID: 28687708, 29444212, 30760892). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This sequence change affects a donor splice site in intron 14 of the EPHB4 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in EPHB4 are known to be pathogenic (PMID: 28687708). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Pathogenic
dbscSNV1_RF
Pathogenic
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 49
DS_DL_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at