chr21-17565677-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001338.5(CXADR):c.1083T>G(p.Asp361Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,611,872 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D361N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001338.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXADR | NM_001338.5 | c.1083T>G | p.Asp361Glu | missense_variant | 7/7 | ENST00000284878.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXADR | ENST00000284878.12 | c.1083T>G | p.Asp361Glu | missense_variant | 7/7 | 1 | NM_001338.5 | P2 | |
CXADR | ENST00000400166.5 | c.*62T>G | 3_prime_UTR_variant | 5/5 | 1 | ||||
CXADR | ENST00000400169.1 | c.1017+66T>G | intron_variant | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249398Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135160
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1459690Hom.: 0 Cov.: 33 AF XY: 0.00000826 AC XY: 6AN XY: 726160
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152182Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 02, 2022 | The c.1083T>G (p.D361E) alteration is located in exon 7 (coding exon 7) of the CXADR gene. This alteration results from a T to G substitution at nucleotide position 1083, causing the aspartic acid (D) at amino acid position 361 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at