3-119537173-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005191.4(CD80):c.664C>T(p.His222Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00994 in 1,613,976 control chromosomes in the GnomAD database, including 105 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0076 ( 4 hom., cov: 32)
Exomes 𝑓: 0.010 ( 101 hom. )
Consequence
CD80
NM_005191.4 missense
NM_005191.4 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 0.125
Genes affected
CD80 (HGNC:1700): (CD80 molecule) The protein encoded by this gene is a membrane receptor that is activated by the binding of CD28 or CTLA-4. The activated protein induces T-cell proliferation and cytokine production. This protein can act as a receptor for adenovirus subgroup B and may play a role in lupus neuropathy. [provided by RefSeq, Aug 2011]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.009736687).
BP6
?
Variant 3-119537173-G-A is Benign according to our data. Variant chr3-119537173-G-A is described in ClinVar as [Benign]. Clinvar id is 774605.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAd at 4 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD80 | NM_005191.4 | c.664C>T | p.His222Tyr | missense_variant | 4/7 | ENST00000264246.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD80 | ENST00000264246.8 | c.664C>T | p.His222Tyr | missense_variant | 4/7 | 1 | NM_005191.4 | P2 | |
CD80 | ENST00000478182.5 | c.664C>T | p.His222Tyr | missense_variant | 4/6 | 1 | P2 | ||
CD80 | ENST00000383669.3 | c.664C>T | p.His222Tyr | missense_variant | 3/4 | 1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00761 AC: 1158AN: 152204Hom.: 4 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
1158
AN:
152204
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.00737 AC: 1850AN: 251054Hom.: 13 AF XY: 0.00725 AC XY: 984AN XY: 135648
GnomAD3 exomes
AF:
AC:
1850
AN:
251054
Hom.:
AF XY:
AC XY:
984
AN XY:
135648
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0102 AC: 14888AN: 1461654Hom.: 101 Cov.: 31 AF XY: 0.00993 AC XY: 7220AN XY: 727146
GnomAD4 exome
AF:
AC:
14888
AN:
1461654
Hom.:
Cov.:
31
AF XY:
AC XY:
7220
AN XY:
727146
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.00760 AC: 1158AN: 152322Hom.: 4 Cov.: 32 AF XY: 0.00706 AC XY: 526AN XY: 74468
GnomAD4 genome
?
AF:
AC:
1158
AN:
152322
Hom.:
Cov.:
32
AF XY:
AC XY:
526
AN XY:
74468
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
47
ALSPAC
AF:
AC:
50
ESP6500AA
AF:
AC:
9
ESP6500EA
AF:
AC:
90
ExAC
?
AF:
AC:
865
Asia WGS
AF:
AC:
3
AN:
3478
EpiCase
AF:
EpiControl
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Uncertain
D;D;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;N
MutationTaster
Benign
N;N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N
REVEL
Benign
Sift
Uncertain
D;D;T
Sift4G
Uncertain
D;D;D
Polyphen
P;P;.
Vest4
MVP
MPC
ClinPred
T
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at