chr14-23357629-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005864.4(EFS):c.1283T>C(p.Val428Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000709 in 1,551,440 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFS | NM_005864.4 | c.1283T>C | p.Val428Ala | missense_variant | 6/6 | ENST00000216733.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFS | ENST00000216733.8 | c.1283T>C | p.Val428Ala | missense_variant | 6/6 | 1 | NM_005864.4 | P1 | |
EFS | ENST00000351354.3 | c.1004T>C | p.Val335Ala | missense_variant | 5/5 | 1 | |||
EFS | ENST00000429593.6 | c.776T>C | p.Val259Ala | missense_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000330 AC: 5AN: 151476Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000141 AC: 3AN: 213196Hom.: 0 AF XY: 0.00000883 AC XY: 1AN XY: 113260
GnomAD4 exome AF: 0.00000429 AC: 6AN: 1399964Hom.: 0 Cov.: 32 AF XY: 0.00000437 AC XY: 3AN XY: 686708
GnomAD4 genome ? AF: 0.0000330 AC: 5AN: 151476Hom.: 0 Cov.: 33 AF XY: 0.0000270 AC XY: 2AN XY: 74018
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 29, 2023 | The c.1283T>C (p.V428A) 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 1283, causing the valine (V) at amino acid position 428 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