chrX-68830124-C-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004429.5(EFNB1):c.128+220C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.052 in 111,093 control chromosomes in the GnomAD database, including 347 homozygotes. There are 1,572 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.052 ( 347 hom., 1572 hem., cov: 23)
Consequence
EFNB1
NM_004429.5 intron
NM_004429.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.0850
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 -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.94).
BP6
Variant X-68830124-C-G is Benign according to our data. Variant chrX-68830124-C-G is described in ClinVar as [Benign]. Clinvar id is 1233937.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFNB1 | NM_004429.5 | c.128+220C>G | intron_variant | ENST00000204961.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFNB1 | ENST00000204961.5 | c.128+220C>G | intron_variant | 1 | NM_004429.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0519 AC: 5760AN: 111044Hom.: 347 Cov.: 23 AF XY: 0.0469 AC XY: 1561AN XY: 33290
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0520 AC: 5775AN: 111093Hom.: 347 Cov.: 23 AF XY: 0.0471 AC XY: 1572AN XY: 33349
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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 | Feb 14, 2019 | - - |
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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at