chrX-68829392-G-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_004429.5(EFNB1):c.-385G>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0119 in 216,004 control chromosomes in the GnomAD database, including 75 homozygotes. There are 669 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.022 ( 73 hom., 646 hem., cov: 24)
Exomes 𝑓: 0.0011 ( 2 hom. 23 hem. )
Consequence
EFNB1
NM_004429.5 5_prime_UTR
NM_004429.5 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.29
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=-0.77).
BP6
?
Variant X-68829392-G-T is Benign according to our data. Variant chrX-68829392-G-T is described in ClinVar as [Benign]. Clinvar id is 1277903.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.074 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFNB1 | NM_004429.5 | c.-385G>T | 5_prime_UTR_variant | 1/5 | ENST00000204961.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFNB1 | ENST00000204961.5 | c.-385G>T | 5_prime_UTR_variant | 1/5 | 1 | NM_004429.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0220 AC: 2463AN: 112038Hom.: 73 Cov.: 24 AF XY: 0.0188 AC XY: 645AN XY: 34256
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GnomAD4 exome AF: 0.00109 AC: 113AN: 103918Hom.: 2 Cov.: 0 AF XY: 0.000760 AC XY: 23AN XY: 30266
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GnomAD4 genome ? AF: 0.0220 AC: 2465AN: 112086Hom.: 73 Cov.: 24 AF XY: 0.0188 AC XY: 646AN XY: 34314
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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 | Mar 16, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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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