rs7865848
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_052820.4(CORO2A):c.201+9049A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0207 in 111,004 control chromosomes in the GnomAD database, including 53 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 0.021 ( 53 hom., cov: 29)
Consequence
CORO2A
NM_052820.4 intron
NM_052820.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.02
Genes affected
CORO2A (HGNC:2255): (coronin 2A) This gene encodes a member of the WD repeat protein family. WD repeats are minimally conserved regions of approximately 40 amino acids typically bracketed by gly-his and trp-asp (GH-WD), which may facilitate formation of heterotrimeric or multiprotein complexes. Members of this family are involved in a variety of cellular processes, including cell cycle progression, signal transduction, apoptosis, and gene regulation. This protein contains 5 WD repeats, and has a structural similarity with actin-binding proteins: the D. discoideum coronin and the human p57 protein, suggesting that this protein may also be an actin-binding protein that regulates cell motility. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]
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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=-1.0).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0207 (2301/111004) while in subpopulation AFR AF= 0.0502 (1492/29706). AF 95% confidence interval is 0.0481. There are 53 homozygotes in gnomad4. There are 1083 alleles in male gnomad4 subpopulation. Median coverage is 29. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd4 at 53 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CORO2A | NM_052820.4 | c.201+9049A>T | intron_variant | ENST00000375077.5 | |||
CORO2A | NM_003389.3 | c.201+9049A>T | intron_variant | ||||
CORO2A | XM_011518986.4 | c.201+9049A>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CORO2A | ENST00000375077.5 | c.201+9049A>T | intron_variant | 1 | NM_052820.4 | P1 | |||
CORO2A | ENST00000343933.9 | c.201+9049A>T | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0207 AC: 2295AN: 110964Hom.: 52 Cov.: 29
GnomAD3 genomes
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.0207 AC: 2301AN: 111004Hom.: 53 Cov.: 29 AF XY: 0.0202 AC XY: 1083AN XY: 53714
GnomAD4 genome
?
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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