19-50725314-C-CGCCCA
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_002975.3(CLEC11A):c.827_831dup(p.Ala278ProfsTer129) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00198 in 1,611,922 control chromosomes in the GnomAD database, including 14 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0015 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0020 ( 12 hom. )
Consequence
CLEC11A
NM_002975.3 frameshift
NM_002975.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.0370
Genes affected
CLEC11A (HGNC:10576): (C-type lectin domain containing 11A) This gene encodes a member of the C-type lectin superfamily. The encoded protein is a secreted sulfated glycoprotein and functions as a growth factor for primitive hematopoietic progenitor cells. An alternative splice variant has been described but its biological nature has not been determined. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 19-50725314-C-CGCCCA is Benign according to our data. Variant chr19-50725314-C-CGCCCA is described in ClinVar as [Likely_benign]. Clinvar id is 785833.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC11A | NM_002975.3 | c.827_831dup | p.Ala278ProfsTer129 | frameshift_variant | 4/4 | ENST00000250340.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC11A | ENST00000250340.9 | c.827_831dup | p.Ala278ProfsTer129 | frameshift_variant | 4/4 | 1 | NM_002975.3 | P1 | |
CLEC11A | ENST00000599973.1 | c.876_880dup | p.Arg294ProfsTer49 | frameshift_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00156 AC: 237AN: 152202Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00166 AC: 391AN: 236204Hom.: 4 AF XY: 0.00174 AC XY: 227AN XY: 130194
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GnomAD4 exome AF: 0.00203 AC: 2956AN: 1459606Hom.: 12 Cov.: 48 AF XY: 0.00201 AC XY: 1461AN XY: 726132
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GnomAD4 genome ? AF: 0.00155 AC: 236AN: 152316Hom.: 2 Cov.: 33 AF XY: 0.00144 AC XY: 107AN XY: 74484
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Mar 29, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.