3-112347589-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000315711.12(CD200):c.453C>A(p.Phe151Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000104 in 1,613,932 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000315711.12 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CD200 | NM_005944.7 | c.453C>A | p.Phe151Leu | missense_variant | 4/6 | ENST00000315711.12 | NP_005935.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CD200 | ENST00000315711.12 | c.453C>A | p.Phe151Leu | missense_variant | 4/6 | 1 | NM_005944.7 | ENSP00000312766 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000518 AC: 13AN: 251154Hom.: 0 AF XY: 0.0000663 AC XY: 9AN XY: 135744
GnomAD4 exome AF: 0.000109 AC: 160AN: 1461688Hom.: 1 Cov.: 32 AF XY: 0.000117 AC XY: 85AN XY: 727144
GnomAD4 genome AF: 0.0000525 AC: 8AN: 152244Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74454
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.528C>A (p.F176L) alteration is located in exon 5 (coding exon 5) of the CD200 gene. This alteration results from a C to A substitution at nucleotide position 528, causing the phenylalanine (F) at amino acid position 176 to be replaced by a leucine (L). 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