chr14-23357453-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_005864.4(EFS):c.1459G>T(p.Val487Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000942 in 1,613,920 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V487A) has been classified as Uncertain significance.
Frequency
Consequence
NM_005864.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFS | NM_005864.4 | c.1459G>T | p.Val487Phe | missense_variant | 6/6 | ENST00000216733.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFS | ENST00000216733.8 | c.1459G>T | p.Val487Phe | missense_variant | 6/6 | 1 | NM_005864.4 | P1 | |
EFS | ENST00000351354.3 | c.1180G>T | p.Val394Phe | missense_variant | 5/5 | 1 | |||
EFS | ENST00000429593.6 | c.952G>T | p.Val318Phe | missense_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152256Hom.: 1 Cov.: 33
GnomAD3 exomes AF: 0.000176 AC: 44AN: 250358Hom.: 0 AF XY: 0.000207 AC XY: 28AN XY: 135532
GnomAD4 exome AF: 0.0000910 AC: 133AN: 1461546Hom.: 1 Cov.: 30 AF XY: 0.000129 AC XY: 94AN XY: 727078
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152374Hom.: 1 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74512
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 27, 2022 | The c.1459G>T (p.V487F) alteration is located in exon 6 (coding exon 6) of the EFS gene. This alteration results from a G to T substitution at nucleotide position 1459, causing the valine (V) at amino acid position 487 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at