4-53273986-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152540.4(SCFD2):c.1151G>A(p.Gly384Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,609,836 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152540.4 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 |
---|---|---|---|---|---|---|---|
SCFD2 | NM_152540.4 | c.1151G>A | p.Gly384Glu | missense_variant | 4/9 | ENST00000401642.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCFD2 | ENST00000401642.8 | c.1151G>A | p.Gly384Glu | missense_variant | 4/9 | 1 | NM_152540.4 | P1 | |
SCFD2 | ENST00000388940.8 | c.1151G>A | p.Gly384Glu | missense_variant | 4/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152144Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000805 AC: 20AN: 248472Hom.: 1 AF XY: 0.000119 AC XY: 16AN XY: 134250
GnomAD4 exome AF: 0.0000240 AC: 35AN: 1457576Hom.: 1 Cov.: 30 AF XY: 0.0000386 AC XY: 28AN XY: 724786
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74444
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 17, 2023 | The c.1151G>A (p.G384E) alteration is located in exon 4 (coding exon 4) of the SCFD2 gene. This alteration results from a G to A substitution at nucleotide position 1151, causing the glycine (G) at amino acid position 384 to be replaced by a glutamic acid (E). 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