chr14-23359432-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005864.4(EFS):c.1046G>T(p.Gly349Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000211 in 1,608,392 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFS | NM_005864.4 | c.1046G>T | p.Gly349Val | missense_variant | 4/6 | ENST00000216733.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFS | ENST00000216733.8 | c.1046G>T | p.Gly349Val | missense_variant | 4/6 | 1 | NM_005864.4 | P1 | |
EFS | ENST00000351354.3 | c.767G>T | p.Gly256Val | missense_variant | 3/5 | 1 | |||
EFS | ENST00000429593.6 | c.539G>T | p.Gly180Val | missense_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000922 AC: 14AN: 151902Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000335 AC: 8AN: 238520Hom.: 0 AF XY: 0.0000537 AC XY: 7AN XY: 130380
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1456490Hom.: 0 Cov.: 35 AF XY: 0.0000193 AC XY: 14AN XY: 724550
GnomAD4 genome ? AF: 0.0000922 AC: 14AN: 151902Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.1046G>T (p.G349V) alteration is located in exon 4 (coding exon 4) of the EFS gene. This alteration results from a G to T substitution at nucleotide position 1046, causing the glycine (G) at amino acid position 349 to be replaced by a valine (V). 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