rs476463
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001281956.2(CSMD2):c.1663+6137C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.186 in 152,054 control chromosomes in the GnomAD database, including 3,515 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 3515 hom., cov: 31)
Consequence
CSMD2
NM_001281956.2 intron
NM_001281956.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.279
Genes affected
CSMD2 (HGNC:19290): (CUB and Sushi multiple domains 2) The protein encoded by this gene is thought to be involved in the control of complement cascade of the immune system. Defects in this gene have been associated with schizophrenia. This gene may act as a tumor suppressor for colorectal cancer. [provided by RefSeq, Jan 2020]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.98).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSMD2 | NM_001281956.2 | c.1663+6137C>T | intron_variant | ENST00000373381.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSMD2 | ENST00000373381.9 | c.1663+6137C>T | intron_variant | 1 | NM_001281956.2 | P2 | |||
CSMD2 | ENST00000373388.7 | c.1543+6137C>T | intron_variant | 1 | |||||
CSMD2 | ENST00000338325.1 | n.900+6137C>T | intron_variant, non_coding_transcript_variant | 1 | |||||
CSMD2 | ENST00000619121.4 | c.1543+6137C>T | intron_variant | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.186 AC: 28286AN: 151936Hom.: 3506 Cov.: 31
GnomAD3 genomes
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151936
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.186 AC: 28320AN: 152054Hom.: 3515 Cov.: 31 AF XY: 0.184 AC XY: 13706AN XY: 74362
GnomAD4 genome
?
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28320
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152054
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31
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13706
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74362
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502
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
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