11-66315278-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_020404.3(CD248):āc.1750A>Gā(p.Ile584Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000519 in 1,540,132 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
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.1750A>G | p.Ile584Val | missense_variant | 1/1 | ENST00000311330.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD248 | ENST00000311330.4 | c.1750A>G | p.Ile584Val | missense_variant | 1/1 | NM_020404.3 | P1 | ||
ENST00000534065.1 | n.140+2286T>C | intron_variant, non_coding_transcript_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000663 AC: 1AN: 150910Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000206 AC: 4AN: 193862Hom.: 0 AF XY: 0.0000390 AC XY: 4AN XY: 102466
GnomAD4 exome AF: 0.00000504 AC: 7AN: 1389222Hom.: 0 Cov.: 31 AF XY: 0.00000439 AC XY: 3AN XY: 683126
GnomAD4 genome AF: 0.00000663 AC: 1AN: 150910Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 73618
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 22, 2023 | The c.1750A>G (p.I584V) alteration is located in exon 1 (coding exon 1) of the CD248 gene. This alteration results from a A to G substitution at nucleotide position 1750, causing the isoleucine (I) at amino acid position 584 to be replaced by a valine (V). 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