17-44868279-CTACTT-C
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP3BP6_Very_StrongBS1BS2
The NM_004247.4(EFTUD2):c.1058+3_1058+7delAAGTA variant causes a splice region, intron change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00642 in 1,613,102 control chromosomes in the GnomAD database, including 37 homozygotes. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_004247.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00519 AC: 789AN: 152118Hom.: 4 Cov.: 31
GnomAD3 exomes AF: 0.00542 AC: 1359AN: 250748Hom.: 4 AF XY: 0.00526 AC XY: 713AN XY: 135536
GnomAD4 exome AF: 0.00655 AC: 9562AN: 1460868Hom.: 33 AF XY: 0.00634 AC XY: 4610AN XY: 726734
GnomAD4 genome AF: 0.00518 AC: 789AN: 152234Hom.: 4 Cov.: 31 AF XY: 0.00512 AC XY: 381AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:6
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This variant is associated with the following publications: (PMID: 23188108, 27895973) -
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EFTUD2: BP4, BS1, BS2 -
not specified Benign:2
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Mandibulofacial dysostosis-microcephaly syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at