chr2-88857564-A-G
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The ENST00000390237.2(IGKC):āc.121T>Cā(p.Trp41Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000159 in 627,750 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 32)
Exomes š: 0.0000016 ( 0 hom. )
Consequence
IGKC
ENST00000390237.2 missense
ENST00000390237.2 missense
Scores
2
Clinical Significance
Conservation
PhyloP100: 7.42
Genes affected
IGKC (HGNC:5716): (immunoglobulin kappa constant) Predicted to enable antigen binding activity and immunoglobulin receptor binding activity. Involved in retina homeostasis. Located in blood microparticle and extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 2-88857564-A-G is Pathogenic according to our data. Variant chr2-88857564-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 29758.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IGKC | ENST00000390237.2 | c.121T>C | p.Trp41Arg | missense_variant | 1/1 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000159 AC: 1AN: 627750Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 342020
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342020
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GnomAD4 genome Cov.: 32
GnomAD4 genome
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32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Recurrent infections associated with rare immunoglobulin isotypes deficiency Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 25, 1985 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.