rs59161567
Variant summary
Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_ModerateBP6_Very_StrongBP7BS1
The NM_006158.5(NEFL):c.423G>A(p.Gln141Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000535 in 1,606,266 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
Consequence
NM_006158.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -15 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NEFL | ENST00000610854.2 | c.423G>A | p.Gln141Gln | synonymous_variant | Exon 1 of 4 | 1 | NM_006158.5 | ENSP00000482169.2 | ||
ENSG00000272157 | ENST00000607735.2 | n.153C>T | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 | |||||
NEFL | ENST00000615973.1 | n.629G>A | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152252Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000720 AC: 17AN: 236198Hom.: 1 AF XY: 0.0000541 AC XY: 7AN XY: 129490
GnomAD4 exome AF: 0.0000461 AC: 67AN: 1453896Hom.: 0 Cov.: 37 AF XY: 0.0000442 AC XY: 32AN XY: 723208
GnomAD4 genome AF: 0.000125 AC: 19AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.000174 AC XY: 13AN XY: 74512
ClinVar
Submissions by phenotype
not provided Benign:1Other:1
This variant is associated with the following publications: (PMID: 12566280) -
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not specified Benign:1
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Charcot-Marie-Tooth disease Benign:1
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Charcot-Marie-Tooth disease type 2E Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at