chr10-68749601-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP2BP4
The NM_018237.4(CCAR1):c.1034G>A(p.Arg345Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00000547 in 1,461,706 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000055 ( 0 hom. )
Consequence
CCAR1
NM_018237.4 missense
NM_018237.4 missense
Scores
4
1
9
Clinical Significance
Conservation
PhyloP100: 6.67
Genes affected
CCAR1 (HGNC:24236): (cell division cycle and apoptosis regulator 1) Enables RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; nuclear receptor coactivator activity; and transcription corepressor activity. Involved in positive regulation of cell migration and positive regulation of cell population proliferation. Acts upstream of or within positive regulation of apoptotic process. Located in nuclear envelope lumen. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, CCAR1
BP4
?
Computational evidence support a benign effect (MetaRNN=0.283975).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCAR1 | NM_018237.4 | c.1034G>A | p.Arg345Gln | missense_variant | 10/25 | ENST00000265872.11 | |
CCAR1 | NM_001282959.2 | c.989G>A | p.Arg330Gln | missense_variant | 9/24 | ||
CCAR1 | NM_001282960.2 | c.989G>A | p.Arg330Gln | missense_variant | 9/24 | ||
CCAR1 | NR_104262.2 | n.1134G>A | non_coding_transcript_exon_variant | 10/24 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCAR1 | ENST00000265872.11 | c.1034G>A | p.Arg345Gln | missense_variant | 10/25 | 1 | NM_018237.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461706Hom.: 0 Cov.: 31 AF XY: 0.00000413 AC XY: 3AN XY: 727162
GnomAD4 exome
AF:
AC:
8
AN:
1461706
Hom.:
Cov.:
31
AF XY:
AC XY:
3
AN XY:
727162
Gnomad4 AFR exome
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2022 | The c.1034G>A (p.R345Q) alteration is located in exon 10 (coding exon 9) of the CCAR1 gene. This alteration results from a G to A substitution at nucleotide position 1034, causing the arginine (R) at amino acid position 345 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Pathogenic
D
Sift4G
Benign
T;T;T;T;T;T
Polyphen
0.0, 1.0, 0.0010
.;B;D;.;B;.
Vest4
MutPred
Loss of glycosylation at P344 (P = 0.0755);Loss of glycosylation at P344 (P = 0.0755);.;.;.;.;
MVP
MPC
1.9
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at