rs6000488
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000395.3(CSF2RB):c.201-169G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.116 in 152,124 control chromosomes in the GnomAD database, including 1,221 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.12 ( 1221 hom., cov: 32)
Consequence
CSF2RB
NM_000395.3 intron
NM_000395.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.418
Genes affected
CSF2RB (HGNC:2436): (colony stimulating factor 2 receptor subunit beta) The protein encoded by this gene is the common beta chain of the high affinity receptor for IL-3, IL-5 and CSF. Defects in this gene have been reported to be associated with protein alveolar proteinosis (PAP). [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
?
Variant 22-36925818-G-A is Benign according to our data. Variant chr22-36925818-G-A is described in ClinVar as [Benign]. Clinvar id is 1288350.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSF2RB | NM_000395.3 | c.201-169G>A | intron_variant | ENST00000403662.8 | |||
LOC105373023 | XR_938230.2 | n.126C>T | non_coding_transcript_exon_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSF2RB | ENST00000403662.8 | c.201-169G>A | intron_variant | 5 | NM_000395.3 | P1 | |||
CSF2RB | ENST00000406230.5 | c.201-169G>A | intron_variant | 1 | |||||
CSF2RB | ENST00000421539.1 | c.-40-169G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.116 AC: 17605AN: 152006Hom.: 1221 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.116 AC: 17621AN: 152124Hom.: 1221 Cov.: 32 AF XY: 0.112 AC XY: 8346AN XY: 74370
GnomAD4 genome
?
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32
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8346
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74370
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254
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3478
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 | GeneDx | Nov 27, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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