NM_020404.3:c.1768C>T
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_020404.3(CD248):c.1768C>T(p.Pro590Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000111 in 1,537,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 17/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020404.3 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Likely_benign. The variant received -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD248 | ENST00000311330.4 | c.1768C>T | p.Pro590Ser | missense_variant | Exon 1 of 1 | 6 | NM_020404.3 | ENSP00000308117.3 | ||
ENSG00000254458 | ENST00000534065.1 | n.140+2268G>A | intron_variant | Intron 1 of 1 | 4 | |||||
ENSG00000254756 | ENST00000820635.1 | n.134+3097G>A | intron_variant | Intron 1 of 3 | ||||||
ENSG00000254756 | ENST00000820636.1 | n.96+3097G>A | intron_variant | Intron 1 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152024Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000210 AC: 4AN: 190458 AF XY: 0.0000398 show subpopulations
GnomAD4 exome AF: 0.0000108 AC: 15AN: 1385530Hom.: 0 Cov.: 31 AF XY: 0.0000117 AC XY: 8AN XY: 681198 show subpopulations
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152024Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74252 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1768C>T (p.P590S) alteration is located in exon 1 (coding exon 1) of the CD248 gene. This alteration results from a C to T substitution at nucleotide position 1768, causing the proline (P) at amino acid position 590 to be replaced by a serine (S). 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