NM_020964.3:c.1399C>T
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_020964.3(EPG5):c.1399C>T(p.Leu467Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00917 in 1,606,370 control chromosomes in the GnomAD database, including 114 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. L467L) has been classified as Likely benign.
Frequency
Consequence
NM_020964.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00754 AC: 1146AN: 151998Hom.: 9 Cov.: 32
GnomAD3 exomes AF: 0.00882 AC: 2195AN: 248792Hom.: 20 AF XY: 0.00976 AC XY: 1317AN XY: 134984
GnomAD4 exome AF: 0.00934 AC: 13578AN: 1454252Hom.: 105 Cov.: 28 AF XY: 0.00973 AC XY: 7045AN XY: 723868
GnomAD4 genome AF: 0.00753 AC: 1145AN: 152118Hom.: 9 Cov.: 32 AF XY: 0.00731 AC XY: 544AN XY: 74368
ClinVar
Submissions by phenotype
not provided Benign:3
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EPG5: BP4, BS1, BS2 -
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Vici syndrome Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at