1-160841715-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_016382.4(CD244):c.248T>A(p.Phe83Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,614,058 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016382.4 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 |
---|---|---|---|---|---|---|---|
CD244 | NM_016382.4 | c.248T>A | p.Phe83Tyr | missense_variant | 2/9 | ENST00000368034.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD244 | ENST00000368034.9 | c.248T>A | p.Phe83Tyr | missense_variant | 2/9 | 1 | NM_016382.4 | P2 | |
CD244 | ENST00000368033.7 | c.248T>A | p.Phe83Tyr | missense_variant | 2/9 | 1 | A2 | ||
CD244 | ENST00000322302.7 | c.248T>A | p.Phe83Tyr | missense_variant | 2/8 | 1 | |||
CD244 | ENST00000492063.5 | c.248T>A | p.Phe83Tyr | missense_variant, NMD_transcript_variant | 2/9 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251430Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135880
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461880Hom.: 2 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 727244
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 23, 2021 | The c.248T>A (p.F83Y) alteration is located in exon 2 (coding exon 2) of the CD244 gene. This alteration results from a T to A substitution at nucleotide position 248, causing the phenylalanine (F) at amino acid position 83 to be replaced by a tyrosine (Y). 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