chr21-17565577-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_001338.5(CXADR):c.983G>A(p.Arg328His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00127 in 1,613,452 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001338.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CXADR | NM_001338.5 | c.983G>A | p.Arg328His | missense_variant | 7/7 | ENST00000284878.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CXADR | ENST00000284878.12 | c.983G>A | p.Arg328His | missense_variant | 7/7 | 1 | NM_001338.5 | P2 | |
CXADR | ENST00000400166.5 | c.721G>A | p.Ala241Thr | missense_variant | 5/5 | 1 | |||
CXADR | ENST00000400165.5 | c.565G>A | p.Ala189Thr | missense_variant | 4/4 | 1 | |||
CXADR | ENST00000400169.1 | c.983G>A | p.Arg328His | missense_variant | 7/8 | 5 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000803 AC: 122AN: 151976Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000968 AC: 243AN: 251134Hom.: 1 AF XY: 0.00111 AC XY: 151AN XY: 135718
GnomAD4 exome AF: 0.00132 AC: 1934AN: 1461358Hom.: 2 Cov.: 33 AF XY: 0.00139 AC XY: 1012AN XY: 727004
GnomAD4 genome ? AF: 0.000802 AC: 122AN: 152094Hom.: 0 Cov.: 31 AF XY: 0.000928 AC XY: 69AN XY: 74364
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 10, 2023 | The c.983G>A (p.R328H) alteration is located in exon 7 (coding exon 7) of the CXADR gene. This alteration results from a G to A substitution at nucleotide position 983, causing the arginine (R) at amino acid position 328 to be replaced by a histidine (H). 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