12-108623395-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The ENST00000550948.2(SELPLG):c.913G>A(p.Val305Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0004 in 1,614,248 control chromosomes in the GnomAD database, including 9 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
ENST00000550948.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SELPLG | NM_003006.4 | c.913G>A | p.Val305Ile | missense_variant | 2/2 | ENST00000550948.2 | NP_002997.2 | |
SELPLG | NM_001206609.2 | c.961G>A | p.Val321Ile | missense_variant | 2/2 | NP_001193538.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SELPLG | ENST00000550948.2 | c.913G>A | p.Val305Ile | missense_variant | 2/2 | 1 | NM_003006.4 | ENSP00000447752 | P2 | |
SELPLG | ENST00000228463.6 | c.961G>A | p.Val321Ile | missense_variant | 2/2 | 2 | ENSP00000228463 | A2 | ||
SELPLG | ENST00000388962.4 | c.883G>A | p.Val295Ile | missense_variant | 2/2 | 5 | ENSP00000373614 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000282 AC: 43AN: 152236Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000835 AC: 210AN: 251454Hom.: 3 AF XY: 0.00113 AC XY: 154AN XY: 135898
GnomAD4 exome AF: 0.000411 AC: 601AN: 1461894Hom.: 9 Cov.: 32 AF XY: 0.000598 AC XY: 435AN XY: 727248
GnomAD4 genome AF: 0.000295 AC: 45AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000443 AC XY: 33AN XY: 74500
ClinVar
Submissions by phenotype
SELPLG-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 11, 2021 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at