12-108623874-GGAGTGGTCTGTGCCTCCGTGGGCACTGGTT-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM4BP6_ModerateBA1
The NM_003006.4(SELPLG):βc.404_433delβ(p.Gln135_Thr144del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 1,611,826 control chromosomes in the GnomAD database, including 30,506 homozygotes. Variant has been reported in ClinVar as Benign (β ).
Frequency
Genomes: π 0.17 ( 2345 hom., cov: 28)
Exomes π: 0.19 ( 28161 hom. )
Consequence
SELPLG
NM_003006.4 inframe_deletion
NM_003006.4 inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.03
Genes affected
SELPLG (HGNC:10722): (selectin P ligand) This gene encodes a glycoprotein that functions as a high affinity counter-receptor for the cell adhesion molecules P-, E- and L- selectin expressed on myeloid cells and stimulated T lymphocytes. As such, this protein plays a critical role in leukocyte trafficking during inflammation by tethering of leukocytes to activated platelets or endothelia expressing selectins. This protein requires two post-translational modifications, tyrosine sulfation and the addition of the sialyl Lewis x tetrasaccharide (sLex) to its O-linked glycans, for its high-affinity binding activity. Aberrant expression of this gene and polymorphisms in this gene are associated with defects in the innate and adaptive immune response. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Apr 2011]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
PM4
?
Nonframeshift variant in NON repetitive region in NM_003006.4.
BP6
?
Variant 12-108623874-GGAGTGGTCTGTGCCTCCGTGGGCACTGGTT-G is Benign according to our data. Variant chr12-108623874-GGAGTGGTCTGTGCCTCCGTGGGCACTGGTT-G is described in ClinVar as [Benign]. Clinvar id is 768578.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELPLG | NM_003006.4 | c.404_433del | p.Gln135_Thr144del | inframe_deletion | 2/2 | ENST00000550948.2 | |
SELPLG | NM_001206609.2 | c.452_481del | p.Gln151_Thr160del | inframe_deletion | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELPLG | ENST00000550948.2 | c.404_433del | p.Gln135_Thr144del | inframe_deletion | 2/2 | 1 | NM_003006.4 | P2 | |
SELPLG | ENST00000228463.6 | c.452_481del | p.Gln151_Thr160del | inframe_deletion | 2/2 | 2 | A2 | ||
SELPLG | ENST00000388962.4 | c.390+14_403del | splice_acceptor_variant, coding_sequence_variant, intron_variant | 2/2 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.166 AC: 25018AN: 150428Hom.: 2332 Cov.: 28
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GnomAD3 exomes AF: 0.176 AC: 44070AN: 249806Hom.: 4074 AF XY: 0.182 AC XY: 24520AN XY: 134992
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GnomAD4 exome AF: 0.190 AC: 278052AN: 1461282Hom.: 28161 AF XY: 0.192 AC XY: 139512AN XY: 726964
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GnomAD4 genome ? AF: 0.167 AC: 25068AN: 150544Hom.: 2345 Cov.: 28 AF XY: 0.168 AC XY: 12386AN XY: 73520
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 22, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at