chr17-44883641-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004247.4(EFTUD2):c.426+8G>A variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 1,610,642 control chromosomes in the GnomAD database, including 289,269 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004247.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFTUD2 | NM_004247.4 | c.426+8G>A | splice_region_variant, intron_variant | ENST00000426333.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFTUD2 | ENST00000426333.7 | c.426+8G>A | splice_region_variant, intron_variant | 1 | NM_004247.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.614 AC: 93373AN: 151964Hom.: 29358 Cov.: 32
GnomAD3 exomes AF: 0.561 AC: 141071AN: 251344Hom.: 40574 AF XY: 0.561 AC XY: 76242AN XY: 135846
GnomAD4 exome AF: 0.594 AC: 866578AN: 1458558Hom.: 259884 Cov.: 33 AF XY: 0.592 AC XY: 429398AN XY: 725742
GnomAD4 genome ? AF: 0.614 AC: 93441AN: 152084Hom.: 29385 Cov.: 32 AF XY: 0.604 AC XY: 44906AN XY: 74360
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genetic Services Laboratory, University of Chicago | - | Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. - |
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 03, 2018 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Mandibulofacial dysostosis-microcephaly syndrome Benign:2
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 30, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at