rs373063662
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_004247.4(EFTUD2):c.1608-17A>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000966 in 1,490,112 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 Likely benign (★★).
Frequency
Genomes: 𝑓 0.00044 ( 0 hom., cov: 31)
Exomes 𝑓: 0.000058 ( 0 hom. )
Consequence
EFTUD2
NM_004247.4 splice_polypyrimidine_tract, intron
NM_004247.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.44
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 -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
?
Variant 17-44860560-T-A is Benign according to our data. Variant chr17-44860560-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 259253.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000442 (67/151658) while in subpopulation AFR AF= 0.00155 (64/41372). AF 95% confidence interval is 0.00124. There are 0 homozygotes in gnomad4. There are 24 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
BS2
?
High AC in GnomAd4 at 67 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFTUD2 | NM_004247.4 | c.1608-17A>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000426333.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFTUD2 | ENST00000426333.7 | c.1608-17A>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_004247.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000442 AC: 67AN: 151568Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000129 AC: 32AN: 247554Hom.: 0 AF XY: 0.000112 AC XY: 15AN XY: 133942
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GnomAD4 exome AF: 0.0000575 AC: 77AN: 1338454Hom.: 0 Cov.: 22 AF XY: 0.0000491 AC XY: 33AN XY: 671986
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GnomAD4 genome ? AF: 0.000442 AC: 67AN: 151658Hom.: 0 Cov.: 31 AF XY: 0.000324 AC XY: 24AN XY: 74078
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 19, 2021 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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