22-21642383-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_022044.3(SDF2L1):c.47G>A(p.Gly16Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000696 in 1,445,110 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. G16R) has been classified as Uncertain significance.
Frequency
Consequence
NM_022044.3 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 |
---|---|---|---|---|---|---|---|
SDF2L1 | NM_022044.3 | c.47G>A | p.Gly16Glu | missense_variant | 1/3 | ENST00000248958.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SDF2L1 | ENST00000248958.5 | c.47G>A | p.Gly16Glu | missense_variant | 1/3 | 1 | NM_022044.3 | P1 | |
SDF2L1 | ENST00000466935.1 | n.30G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000427 AC: 65AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000370 AC: 21AN: 56790Hom.: 0 AF XY: 0.000244 AC XY: 8AN XY: 32744
GnomAD4 exome AF: 0.000728 AC: 941AN: 1292810Hom.: 0 Cov.: 31 AF XY: 0.000699 AC XY: 443AN XY: 633880
GnomAD4 genome ? AF: 0.000427 AC: 65AN: 152300Hom.: 0 Cov.: 32 AF XY: 0.000403 AC XY: 30AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2021 | The c.47G>A (p.G16E) alteration is located in exon 1 (coding exon 1) of the SDF2L1 gene. This alteration results from a G to A substitution at nucleotide position 47, causing the glycine (G) at amino acid position 16 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