9-127815251-A-C
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001114753.3(ENG):c.*431T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000695 in 172,664 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00015 ( 0 hom. )
Consequence
ENG
NM_001114753.3 3_prime_UTR
NM_001114753.3 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.897
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 Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 9-127815251-A-C is Benign according to our data. Variant chr9-127815251-A-C is described in ClinVar as [Benign]. Clinvar id is 1695265.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.0000591 (9/152316) while in subpopulation SAS AF= 0.00166 (8/4826). AF 95% confidence interval is 0.000824. There are 0 homozygotes in gnomad4. There are 7 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 9 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ENG | NM_001114753.3 | c.*431T>G | 3_prime_UTR_variant | Exon 15 of 15 | ENST00000373203.9 | NP_001108225.1 | ||
ENG | NM_000118.4 | c.*666T>G | 3_prime_UTR_variant | Exon 14 of 14 | NP_000109.1 | |||
ENG | NM_001278138.2 | c.*431T>G | 3_prime_UTR_variant | Exon 15 of 15 | NP_001265067.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ENG | ENST00000373203 | c.*431T>G | 3_prime_UTR_variant | Exon 15 of 15 | 1 | NM_001114753.3 | ENSP00000362299.4 | |||
ENG | ENST00000344849 | c.*666T>G | 3_prime_UTR_variant | Exon 14 of 14 | 1 | ENSP00000341917.3 | ||||
ENG | ENST00000480266 | c.*431T>G | 3_prime_UTR_variant | Exon 15 of 15 | 2 | ENSP00000479015.1 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152198Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000147 AC: 3AN: 20348Hom.: 0 Cov.: 0 AF XY: 0.000192 AC XY: 2AN XY: 10434
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.0000940 AC XY: 7AN XY: 74484
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jun 01, 2022 | ENG: BS1, BS2 - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at