rs36080296

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3

The NM_000212.3(ITGB3):​c.197T>C​(p.Leu66Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,890 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 6.8e-7 ( 0 hom. )

Consequence

ITGB3
NM_000212.3 missense

Scores

9
6
3

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.25
Variant links:
Genes affected
ITGB3 (HGNC:6156): (integrin subunit beta 3) The ITGB3 protein product is the integrin beta chain beta 3. Integrins are integral cell-surface proteins composed of an alpha chain and a beta chain. A given chain may combine with multiple partners resulting in different integrins. Integrin beta 3 is found along with the alpha IIb chain in platelets. Integrins are known to participate in cell adhesion as well as cell-surface mediated signalling. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 3 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.79

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ITGB3NM_000212.3 linkc.197T>C p.Leu66Pro missense_variant Exon 3 of 15 ENST00000559488.7 NP_000203.2 P05106-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ITGB3ENST00000559488.7 linkc.197T>C p.Leu66Pro missense_variant Exon 3 of 15 1 NM_000212.3 ENSP00000452786.2 P05106-1
ITGB3ENST00000571680.1 linkc.197T>C p.Leu66Pro missense_variant Exon 3 of 9 1 ENSP00000461626.1 I3L4X8
ENSG00000259753ENST00000560629.1 linkn.161T>C non_coding_transcript_exon_variant Exon 3 of 18 2 ENSP00000456711.2 H3BM21
ITGB3ENST00000696963.1 linkc.197T>C p.Leu66Pro missense_variant Exon 3 of 14 ENSP00000513002.1 P05106-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461890
Hom.:
0
Cov.:
33
AF XY:
0.00
AC XY:
0
AN XY:
727248
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.58
BayesDel_addAF
Pathogenic
0.44
D
BayesDel_noAF
Pathogenic
0.39
CADD
Pathogenic
26
DANN
Pathogenic
1.0
DEOGEN2
Pathogenic
0.81
D;.
Eigen
Pathogenic
0.72
Eigen_PC
Pathogenic
0.72
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Uncertain
0.94
D;D
M_CAP
Uncertain
0.25
D
MetaRNN
Pathogenic
0.79
D;D
MetaSVM
Uncertain
0.74
D
MutationAssessor
Uncertain
2.4
M;.
PrimateAI
Uncertain
0.62
T
PROVEAN
Uncertain
-2.8
D;.
Sift
Benign
0.14
T;.
Sift4G
Benign
0.31
T;T
Polyphen
1.0
D;.
Vest4
0.72
MutPred
0.47
Loss of stability (P = 0.0281);Loss of stability (P = 0.0281);
MVP
0.97
MPC
1.6
ClinPred
0.94
D
GERP RS
5.9
Varity_R
0.83
gMVP
0.97

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-45360751; API