chr17-44852051-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_004247.4(EFTUD2):c.2716-234C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00377 in 152,060 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0038 ( 4 hom., cov: 31)
Consequence
EFTUD2
NM_004247.4 intron
NM_004247.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.244
Genes affected
EFTUD2 (HGNC:30858): (elongation factor Tu GTP binding domain containing 2) This gene encodes a GTPase which is a component of the spliceosome complex which processes precursor mRNAs to produce mature mRNAs. Mutations in this gene are associated with mandibulofacial dysostosis with microcephaly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]
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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=-0.69).
BP6
?
Variant 17-44852051-G-A is Benign according to our data. Variant chr17-44852051-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1198451.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00377 (573/152060) while in subpopulation AFR AF= 0.0136 (563/41458). AF 95% confidence interval is 0.0127. There are 4 homozygotes in gnomad4. There are 285 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd at 571 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFTUD2 | NM_004247.4 | c.2716-234C>T | intron_variant | ENST00000426333.7 | |||
EFTUD2 | NM_001142605.2 | c.2611-234C>T | intron_variant | ||||
EFTUD2 | NM_001258353.2 | c.2716-234C>T | intron_variant | ||||
EFTUD2 | NM_001258354.2 | c.2686-234C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFTUD2 | ENST00000426333.7 | c.2716-234C>T | intron_variant | 1 | NM_004247.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00376 AC: 571AN: 151942Hom.: 4 Cov.: 31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00377 AC: 573AN: 152060Hom.: 4 Cov.: 31 AF XY: 0.00383 AC XY: 285AN XY: 74352
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 27, 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
Find out detailed SpliceAI scores and Pangolin per-transcript scores at