3-119537166-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_005191.4(CD80):c.671G>A(p.Arg224Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,614,004 control chromosomes in the GnomAD database, including 2 homozygotes. 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 (★).
Frequency
Consequence
NM_005191.4 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 |
---|---|---|---|---|---|---|---|
CD80 | NM_005191.4 | c.671G>A | p.Arg224Lys | missense_variant | 4/7 | ENST00000264246.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD80 | ENST00000264246.8 | c.671G>A | p.Arg224Lys | missense_variant | 4/7 | 1 | NM_005191.4 | P2 | |
CD80 | ENST00000478182.5 | c.671G>A | p.Arg224Lys | missense_variant | 4/6 | 1 | P2 | ||
CD80 | ENST00000383669.3 | c.671G>A | p.Arg224Lys | missense_variant | 3/4 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152262Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251010Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135632
GnomAD4 exome AF: 0.0000308 AC: 45AN: 1461742Hom.: 2 Cov.: 31 AF XY: 0.0000481 AC XY: 35AN XY: 727170
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152262Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74394
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.671G>A (p.R224K) alteration is located in exon 4 (coding exon 3) of the CD80 gene. This alteration results from a G to A substitution at nucleotide position 671, causing the arginine (R) at amino acid position 224 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