chr14-23357330-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005864.4(EFS):c.1582G>A(p.Gly528Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000534 in 1,611,764 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFS | NM_005864.4 | c.1582G>A | p.Gly528Ser | missense_variant | 6/6 | ENST00000216733.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFS | ENST00000216733.8 | c.1582G>A | p.Gly528Ser | missense_variant | 6/6 | 1 | NM_005864.4 | P1 | |
EFS | ENST00000351354.3 | c.1303G>A | p.Gly435Ser | missense_variant | 5/5 | 1 | |||
EFS | ENST00000429593.6 | c.1075G>A | p.Gly359Ser | missense_variant | 6/6 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000322 AC: 49AN: 152226Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250466Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135460
GnomAD4 exome AF: 0.0000254 AC: 37AN: 1459420Hom.: 0 Cov.: 30 AF XY: 0.0000276 AC XY: 20AN XY: 725488
GnomAD4 genome AF: 0.000322 AC: 49AN: 152344Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74498
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2022 | The c.1582G>A (p.G528S) alteration is located in exon 6 (coding exon 6) of the EFS gene. This alteration results from a G to A substitution at nucleotide position 1582, causing the glycine (G) at amino acid position 528 to be replaced by a serine (S). 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