1-169595987-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_003005.4(SELP):c.2039G>A(p.Gly680Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000093 in 1,613,748 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003005.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SELP | NM_003005.4 | c.2039G>A | p.Gly680Glu | missense_variant | Exon 12 of 17 | ENST00000263686.11 | NP_002996.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251400Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135880
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461626Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727136
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152122Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2039G>A (p.G680E) alteration is located in exon 12 (coding exon 12) of the SELP gene. This alteration results from a G to A substitution at nucleotide position 2039, causing the glycine (G) at amino acid position 680 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