chr1-160831382-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_016382.4(CD244):c.1063C>T(p.Arg355Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00133 in 1,614,104 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R355H) has been classified as Uncertain significance.
Frequency
Consequence
NM_016382.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD244 | NM_016382.4 | c.1063C>T | p.Arg355Cys | missense_variant | 9/9 | ENST00000368034.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD244 | ENST00000368034.9 | c.1063C>T | p.Arg355Cys | missense_variant | 9/9 | 1 | NM_016382.4 | P2 | |
CD244 | ENST00000368033.7 | c.1078C>T | p.Arg360Cys | missense_variant | 9/9 | 1 | A2 | ||
CD244 | ENST00000322302.7 | c.787C>T | p.Arg263Cys | missense_variant | 8/8 | 1 | |||
CD244 | ENST00000492063.5 | c.*217C>T | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000762 AC: 116AN: 152208Hom.: 3 Cov.: 33
GnomAD3 exomes AF: 0.00273 AC: 685AN: 251146Hom.: 9 AF XY: 0.00377 AC XY: 512AN XY: 135744
GnomAD4 exome AF: 0.00139 AC: 2035AN: 1461778Hom.: 35 Cov.: 30 AF XY: 0.00194 AC XY: 1408AN XY: 727198
GnomAD4 genome ? AF: 0.000768 AC: 117AN: 152326Hom.: 3 Cov.: 33 AF XY: 0.00119 AC XY: 89AN XY: 74492
ClinVar
Submissions by phenotype
CD244-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 08, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at