chrX-68830139-C-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PP3_ModerateBP6_ModerateBA1
The NM_004429.5(EFNB1):c.128+235C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.303 in 110,595 control chromosomes in the GnomAD database, including 3,972 homozygotes. There are 9,572 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.30 ( 3972 hom., 9572 hem., cov: 23)
Consequence
EFNB1
NM_004429.5 intron
NM_004429.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.891
Genes affected
EFNB1 (HGNC:3226): (ephrin B1) The protein encoded by this gene is a type I membrane protein and a ligand of Eph-related receptor tyrosine kinases. It may play a role in cell adhesion and function in the development or maintenance of the nervous system. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PP3
?
Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
BP6
?
Variant X-68830139-C-G is Benign according to our data. Variant chrX-68830139-C-G is described in ClinVar as [Benign]. Clinvar id is 1278690.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFNB1 | NM_004429.5 | c.128+235C>G | intron_variant | ENST00000204961.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFNB1 | ENST00000204961.5 | c.128+235C>G | intron_variant | 1 | NM_004429.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.303 AC: 33524AN: 110542Hom.: 3974 Cov.: 23 AF XY: 0.291 AC XY: 9562AN XY: 32874
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.303 AC: 33516AN: 110595Hom.: 3972 Cov.: 23 AF XY: 0.291 AC XY: 9572AN XY: 32937
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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 | GeneDx | Nov 10, 2018 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at