11-66315433-A-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020404.3(CD248):c.1595T>A(p.Met532Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000471 in 1,613,352 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD248 | NM_020404.3 | c.1595T>A | p.Met532Lys | missense_variant | 1/1 | ENST00000311330.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD248 | ENST00000311330.4 | c.1595T>A | p.Met532Lys | missense_variant | 1/1 | NM_020404.3 | P1 | ||
ENST00000534065.1 | n.140+2441A>T | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.000329 AC: 50AN: 151782Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000598 AC: 15AN: 250908Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135664
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461570Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727048
GnomAD4 genome ? AF: 0.000329 AC: 50AN: 151782Hom.: 0 Cov.: 32 AF XY: 0.000324 AC XY: 24AN XY: 74136
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2023 | The c.1595T>A (p.M532K) alteration is located in exon 1 (coding exon 1) of the CD248 gene. This alteration results from a T to A substitution at nucleotide position 1595, causing the methionine (M) at amino acid position 532 to be replaced by a lysine (K). 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