chr14-23357452-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_005864.4(EFS):c.1460T>C(p.Val487Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,613,802 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V487F) has been classified as Uncertain significance.
Frequency
Consequence
NM_005864.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFS | NM_005864.4 | c.1460T>C | p.Val487Ala | missense_variant | 6/6 | ENST00000216733.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFS | ENST00000216733.8 | c.1460T>C | p.Val487Ala | missense_variant | 6/6 | 1 | NM_005864.4 | P1 | |
EFS | ENST00000351354.3 | c.1181T>C | p.Val394Ala | missense_variant | 5/5 | 1 | |||
EFS | ENST00000429593.6 | c.953T>C | p.Val318Ala | missense_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000722 AC: 11AN: 152254Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 250342Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135516
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461548Hom.: 0 Cov.: 30 AF XY: 0.0000124 AC XY: 9AN XY: 727074
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.0000807 AC XY: 6AN XY: 74390
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 19, 2022 | The c.1460T>C (p.V487A) alteration is located in exon 6 (coding exon 6) of the EFS gene. This alteration results from a T to C substitution at nucleotide position 1460, causing the valine (V) at amino acid position 487 to be replaced by an alanine (A). 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