rs2289674
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_004247.4(EFTUD2):c.762T>C(p.Thr254Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.2 in 1,613,850 control chromosomes in the GnomAD database, including 33,798 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_004247.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.201 AC: 30547AN: 151982Hom.: 3356 Cov.: 31
GnomAD3 exomes AF: 0.170 AC: 42782AN: 251356Hom.: 3932 AF XY: 0.169 AC XY: 22918AN XY: 135836
GnomAD4 exome AF: 0.200 AC: 292605AN: 1461750Hom.: 30431 Cov.: 33 AF XY: 0.197 AC XY: 142917AN XY: 727172
GnomAD4 genome AF: 0.201 AC: 30580AN: 152100Hom.: 3367 Cov.: 31 AF XY: 0.195 AC XY: 14515AN XY: 74380
ClinVar
Submissions by phenotype
not specified Benign:4
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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. -
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not provided Benign:3
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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