1-169606969-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003005.4(SELP):c.1499C>T(p.Ser500Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000219 in 1,613,328 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_003005.4 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 |
---|---|---|---|---|---|---|---|
SELP | NM_003005.4 | c.1499C>T | p.Ser500Phe | missense_variant | 9/17 | ENST00000263686.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELP | ENST00000263686.11 | c.1499C>T | p.Ser500Phe | missense_variant | 9/17 | 1 | NM_003005.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00112 AC: 170AN: 152166Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000288 AC: 72AN: 250258Hom.: 0 AF XY: 0.000207 AC XY: 28AN XY: 135242
GnomAD4 exome AF: 0.000126 AC: 184AN: 1461044Hom.: 0 Cov.: 31 AF XY: 0.000107 AC XY: 78AN XY: 726786
GnomAD4 genome AF: 0.00111 AC: 169AN: 152284Hom.: 1 Cov.: 32 AF XY: 0.00125 AC XY: 93AN XY: 74464
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Mar 30, 2021 | SELP NM_003005.3 exon 9 p.Ser500Phe (c.1499C>T): This variant has not been reported in the literature but is present in 0.3% (93/24910) of African alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/1-169576207-G-A?dataset=gnomad_r2_1). Evolutionary conservation suggests that this variant may not impact the protein; computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at